Speaking on RT?? radio, the minister said it would not be possible to get rid of the Health Service Executive structure this year.
He said he wanted to focus on reforms that improve GP practices and building and developing hospital groups.
Mr Varadkar said the 500m euros overrun in healthcare spending was due mainly to a significant increase in the number of people using services this year.
He also said he could not put a deadline on when free GP care for children under six would be available.
When asked if it would be in place as promised by the end of this year, he said: "I can't say that for certain.
"That depends on how the talks and negotiations go with the IMO (Irish Medical Organisation). It is very important to me that we bring GPs with us.
"This is a huge opportunity to put resources back into general practice, I hope they see that, and as well as that, it's an opportunity to change the way we provide healthcare."
Mr Varadkar said he hoped to have a report from an expert group by the end of this month looking at whether medical cards should be issued to people on the basis of their medical condition.
The minister said he would have to see what the group proposed, whether it was affordable and then discuss it in the context of the budget.
He also said the issue of tax relief on health insurance was an issue for Finance Minister Michael Noonan.

The research says the Trojan exploited a previously unknown vulnerability embedded in Word files, allowing Duqu to modify computers' security protection.
The code is believed to have been designed to gather intelligence from industrial control-systems.
Microsoft says it is preparing a software patch to address the issue.
The Laboratory of Cryptography and Systems Security (Crysys) at Budapest University made the discovery.
"We carefully analysed the available forensics data from the original incident where Duqu was uncovered," Dr Boldizsar Bencsath, who led the investigation, told the BBC.
"We found suspicious files that we further analysed, and in one case, we were able to prove that the file contains the installer of Duqu and it uses a zero-day exploit."
A zero-day exploit is a computer threat that make use of a previously unknown software error to allow the attacker to gain permissions they should not have.
Dr Bencsath added that it is possible that Duqu may also be installed by other means, but he had not found any evidence to suggest it.
The news is being publicised by the internet security firm Symantec.
It says that it has confirmed the Duqu infection at six different computer networks belonging to unidentified organisations across a total of eight countries. They include Iran, India, France and Ukraine.
In addition other security firms have reported suspected infections in a further four countries, including the UK.
Duqu has been compared to last year's Stuxnet worm attack, but Symantec says they operate in two distinct ways.
"Stuxnet was about spreading as far and as wide as possible to hunt down systems that could pass on control of industrial organisations - such as nuclear power plants," said Greg Day, Symantec's director of security strategy.
"Duqu has specifically targeted a number of organisations looking to scan across their internal systems, gather intelligence and pass it back out.
"The sort of things it's collecting are design documents and other information that could be the reconnaissance for a further attack."
So far neither Symantec nor Crysys have been able to trace who is receiving the data. Efforts to address the exploit are ongoing.
"Microsoft is working with our partners to provide protections for a vulnerability used in targeted attempts to infect computers with the Duqu malware," a company statement said.
"We will be providing a security update for customers through our update process."
Experts say these types of focused attacks appear to be on the rise.
Earlier this week Symantec reported that 29 chemicals firms had been targeted by a separate Trojan named PoisonIvy.
"Industrial espionage is the natural evolution from cybercrime," said Mr Day.
"Cybercrime is like pick pocketing. But these latest threats are like great train robberies, where the attackers have taken time to understand the intended victim and have a carefully constructed plan to rob them."
Irish Health Minister Leo Varadkar has said the timeframe for the reform of the country's health service was overambitious from the start.
[NEXT_CONCEPT]
The Duqu computer infection was spread with the help of an infected Microsoft Word document, according to a report.