Child Soldiers International and ForcesWatch claim it costs the Ministry of Defence (MoD) twice as much to train a 16-year-old as it does an adult.
That is due to longer training and a higher drop-out rate, they say.
The MoD said it did not recognise figures in the report and it "ignores the benefits" for young people.
Using figures presented to Parliament in 2011, the report said it cost an "estimated" £88,985 to recruit, train and pay new soldiers aged 16 and 17, compared with £42,818 for each adult recruit.
It said initial training for under-18s lasted either 23 or 50 weeks, depending on their chosen trade and where they were trained, whereas adult training takes 14 weeks.
The calculations included £10,000 to recruit each person, irrespective of age. The other costs covered training, accommodation, meals, welfare, health, salary and other support per Army recruit in 2010-11.
Army personnel can be deployed once they turn 18 - which the two groups said meant that "at any one time, approximately 150 soldiers are fully trained but too young to be deployed."
They added that it costs approximately £2.65m to pay the salaries of these un-soldiers, which it said were each paid a salary of £17,690.
The report said the drop-out rate for minors was 36.6% compared with 28.3% for adults, the report said.
But it added that under-18s who completed their training were likely to serve for an average of 10 years, compared with seven-and-a-half years for adult recruits.
The report suggested taxpayers would save between £81.5m and £94m if all recruits were aged 18 and over.
Its authors also say the UK is becoming "increasingly isolated" internationally in continuing with the practice - no other country in Europe recruits from such a young age - and are calling on the MoD to raise the Army recruitment age to 18.
David Gee, of ForcesWatch, said recruiting under-18s into the Army was "a practice from a bygone era".
"It's not just young recruits who pay the price for outdated MoD policies - taxpayers do too," he said.
"And so does the Army when it finds itself undermanned on the front line because so many minors have dropped out of training."
An MoD spokesman said it continued "to actively recruit across all age groups".
"As part of our duty of care to our recruits, no young person under the age of 18 years may join our armed forces without the formal written consent of their parent or guardian," he added.
"There are currently no plans to revisit the government's recruitment policy for under-18s, which is fully compliant with United Nations conventions."
One former serviceman said that joining the armed forces as a teenager was "a good thing for young people".
Jason Hardick, from Maidenhead, Berkshire, told the BBC: "It gives you self-confidence, self-discipline and a certain self-determination.  You never want to fail, you always want to move forward."
He joined two weeks after his 16th birthday, and stayed for 10 years, only leaving to get married.
"I had a brilliant time, it's a good thing for young people to do and I was the youngest of my intake."
The "outdated" practice of recruiting 16-year-olds into the Army is wasting up to £94m a year and should stop, two human rights groups have said.