However, it recommended no action be taken against him, by majority verdict.
Four members cleared him from any wrongdoing, while three others, all Al Wefaq members, recommended disciplinary action.
One accusation made by Al Wefaq was that he appointed one of two suspended hospital consultants as head of the medical team for last month’s Gulf Air Bahrain Grand Prix.
He was also accused of allowing two senior ministry officials, who own a pharmaceutical company and a group of pharmacies, to continue their duties despite a conflict of interest when dealing with tenders for supplies.
Another allegation was that the minister appointed the chairman of a medical probe committee, who had been subjected to a similar investigation, and then cancelling it after the situation was revealed, to protect him.
Dr Al Hamer had earlier said he had simply used his right as minister to reduce the punishment for both consultants.
He said the accusation that one was appointed as head of the medical team for the Grand Prix was "false" and "baseless".
He said it was the Tender Board, not the ministry, which decided who gets supply contracts.
He said he had asked for legal advice on whether the two officials were allowed to enter bids if they own shares and was told that there was no problem since the employees would not be bidding directly.
He also said the allegation about the medical probe committee, which MPs claimed had been cancelled or halted, had no basis.
Parliamentary panel chairman Dr Ali Ahmed said the minister had been cleared of all irregularities because of his strong defence against the allegations during questioning.
"With regard to first accusation, he formed a new probe committee to discuss punishments for the doctors after they submitted grievances and the new panel recommended lower punishments, which he endorsed.
"Our panel also found that there was no irregularity as the minister had checked with legal consultants to ensure that there was no conflict of interest and that they had a right to have shares in their company and continue their duties in the ministry.
"The third accusation was found to be baseless because there was no evidence that the minister had halted or cancelled the medical probe committee.
"He just removed its chairman when hearing about his alleged involvement in a similar investigation."
Committee vice chairman and Al Wefaq MP Dr Abdali Hassan said since his bloc was outnumbered in the committee, any future action against Dr Al Hamer was unlikely.
"Even if he is guilty, it is very difficult to recommend any action because of the number disadvantage in the committee and parliament when the report was put to vote.
"As a bloc, we just wanted to reveal to the public the irregularities committed by the minister.
"Any action is recommended against him or not is not an issue because people now know the truth.
"The panel addressed the issue professionally, despite the vote being otherwise," Mr Hassan said.
