Vaccination, Ethics and Morals During the present times, there is an excessive need to vaccinate people, but what I have noticed is that when one wishes to scrutinize this action, when one wants to ask viable, pertinent and objective questions regarding vaccination those emotionally intelligent, explorative endeavours are often shutdown and the person given the label of 'anti vaxxer' and 'conspiracy theorist'; the freedom to engage in a healthy dialogue is severely compromised. At the same time, I respect that people are afraid and in need to find a solution to the current issue.

In the sutras, we can find analogies that describe the Buddha as the doctor, knowledge of the Dharma as the medicine, monastics as the nursing staff, and all people as the patients. According to this medical analogy, Buddhism is considered a medication with a broad meaning - a medication that can cure the ailments in all aspects of life. In general, but with exceptions, Western medicine functions within a much smaller framework. Western medicine typically approaches illness through physical symptoms. This approach tends to temporarily reduce the suffering and remove the symptoms for a period, but a lack of symptoms does not mean that the root cause has been identified and removed. Therefore, the complete elimination of the disease has not occurred. Buddhism offers patients not only symptomatic relief, but also spiritual guidance to ensure overall and long-lasting health.
While Western researchers have conducted massive studies on pathology,
pharmacology, immunology, and anatomy, enabling them to develop more
sophisticated medical techniques, scientists still doubt that religion
can help explain the cause of a disease. Without validating the role
of religion in disease, scientists remain quite distant from the
definition of disease, its causes, and its treatments as understood
from a religious perspective. According to Buddhism, it is not enough
to approach to medicine in a manner that simply eradicates symptoms;
the spiritual aspect of disease and its mind-based causes and remedies
must be the primary consideration.
Taken from the Buddhist Academy

As a practising Buddhist, it's my view that a person should uphold the ultimate position on what they choose to accept into their body. However, I'm prepared to look at this from other viewpoints.
From a Buddhist perspective, should choosing to have a vaccine under these interesting but challenging times be a discernment that concerns just our own body, or a discernment that should include others too?
From a Buddhist perspective, how does one reconcile with the huge moral and ethical shortcomings that allow pharmaceutical companies to indemnify themselves from any Ill effects caused by vaccination?
The monastic rules of the Vinaya has rules pertaining to food, lodging, medicine, conduct etc. There are rules pertaining to medical care. The Buddha ate, slept, wore robes, took medicine when he was ill etc.
The Middle Way of the Buddha avoids both extreme indulgence and extreme asceticism. It includes moderation in food, healthcare and living. To neglect healthcare is to go against the Middle Way of moderation.
From Kucchivikara-vatthu of the Theravada Vinaya, the Buddha taught:

&quot;A sick person endowed with five qualities is hard to tend to: he does
what is not amenable to his cure; he does not know the proper amount
in things amenable to his cure; he does not take his medicine; he does
not tell his symptoms, as they actually are present, to the nurse
desiring his welfare, saying that they are worse when they are worse,
improving when they are improving, or remaining the same when they are
remaining the same; and he is not the type who can endure bodily
feelings that are painful, fierce, sharp, wracking, repellent,
disagreeable, life-threatening. A sick person endowed with these five
qualities is hard to tend to.
&quot;A sick person endowed with five qualities is easy to tend to: he does
what is amenable to his cure; he knows the proper amount in things
amenable to his cure; he takes his medicine; he tells his symptoms, as
they actually are present, to the nurse desiring his welfare, saying
that they are worse when they are worse, improving when they are
improving, or remaining the same when they are remaining the same; and
he is the type who can endure bodily feelings that are painful,
fierce, sharp, wracking, repellent, disagreeable, life-threatening. A
sick person endowed with these five qualities is easy to tend to.

Based on this Vinaya quote, I would say that the Buddha himself would have wanted his followers to practice moderation, and accept the advice of healthcare professionals and the government when dealing with the Covid-19 pandemic.
Of course, they should not accept advice blindly but they should ask questions and clarify their doubts before they accept the advice if they see fit, as taught in the Kalama Sutta (below):

&quot;So, as I said, Kalamas: 'Don't go by reports, by legends, by
traditions, by scripture, by logical conjecture, by inference, by
analogies, by agreement through pondering views, by probability, or by
the thought, &quot;This contemplative is our teacher.&quot; When you know for
yourselves that, &quot;These qualities are unskillful; these qualities are
blameworthy; these qualities are criticized by the wise; these
qualities, when adopted &amp; carried out, lead to harm &amp; to suffering&quot; —
then you should abandon them.' Thus was it said. And in reference to
this was it said.
&quot;Now, Kalamas, don't go by reports, by legends, by traditions, by
scripture, by logical conjecture, by inference, by analogies, by
agreement through pondering views, by probability, or by the thought,
'This contemplative is our teacher.' When you know for yourselves
that, 'These qualities are skillful; these qualities are blameless;
these qualities are praised by the wise; these qualities, when adopted
&amp; carried out, lead to welfare &amp; to happiness' — then you should enter
&amp; remain in them.

Also, spreading misinformation about Covid-19, masks and vaccines is against the fourth precept of not speaking falsehood.
Wearing a surgical mask is more for the wearer to avoid spreading pathogens to others, than for the wearer's own protection from contracting an infectious disease. As such, wearing a mask with the explicit intention of reducing others' suffering, is also an expression of compassion (karuna).
Getting vaccinated with the intention of preventing others, especially the high risk group, from becoming infected, is also an expression of compassion (karuna).
The quote from DN 26 below, also shows that the Buddha did not promote anarchy or civil disobedience. He stated that the wheel-turning monarch should provide just protection and security to his subjects and also care for their welfare.

‘But sire, what are the noble duties of a wheel-turning monarch?’
‘Well then, my dear, relying only on principle—honoring, respecting,
and venerating principle, having principle as your flag, banner, and
authority — provide just protection and security for your court,
troops, aristocrats, vassals, brahmins and householders, people of
town and country, ascetics and brahmins, beasts and birds. Do not let
injustice prevail in the realm. Pay money to the penniless in the
realm.

I would even say that a responsible Buddhist should support his or her government and follow its advice (after clarifying it), if the government is discernibly doing the right thing, and if its advice is in accordance with the five precepts, Right Action, Right Speech and Right Livelihood. For e.g. conscription into military service is against Right Livelihood, and should be declined.