The Al Wefaq parliamentary bloc sought the probe into three main allegations against Dr Al Hamer.
One is that he appointed one of two suspended hospital consultants as head of the medical team for last month’s Gulf Air Bahrain Grand Prix.
Dr Al Hamer is also accused of allowing two senior ministry officials, who own a pharmaceutical company and group of pharmacies, to continue their duties despite a conflict of interest when dealing with tenders for supplies.
He is also accused of appointing a chairman of a medical probe committee who had himself been subjected to a similar investigation, then cancelling the committee after this was revealed, to protect the chairman.
But Dr Al Hamer said after being questioned that he was confident that MPs would find the allegations groundless.
"As a minister I used my right to reduce the punishment of both consultants and the claim that one was appointed as head of the medical team for the Bahrain Grand Prix is false and baseless," he said.
Regarding the second allegation, Dr Al Hamer said it was the Tender board, not the ministry which decided who got supply contracts.
"I have asked those behind the questioning to present documents showing irregularity in the way bids were chosen, but they failed to do so," he said.
"The fact that the ministry’s spending has increased over the years on purchases is due to need.
"I asked for legal advice on whether the two officials were allowed to enter bids if they own shares and the response was that there is no problem since it was not the employees bidding directly."
Dr Al Hamer said there was no basis to the allegations over the medical probe committee.
"There is no evidence that the committee has been cancelled or halted and I wish that the MPs would check facts before making accusations," he said.
Dr Al Hamer said that the documents the MPs presented were too weak for an investigation to be built on.
"Such accusations have a negative impact on the country and its people and hopefully this will never happen again," he said.
The committee will meet on either Sunday or Monday to discuss whether to recommend further action in parliament.
