The New Straits Times newspaper did not name the tainted duo but said both medal-winning athletes' initial samples had returned positive results for banned substances from the multi-sports event in Jakarta and Palembang.
"I am shocked to hear that two of our athletes have failed dope tests. I still am not sure how this has happened and I am waiting for an answer from the associations," sports minister Ahmad Shabery Cheek was quoted as saying in the newspaper.
"This responsibility falls on the national associations and the fact that they are keeping silent shows they have no clue what to do over this matter."
The report said that one of the athletes was a member of Malaysia's victorious 4x400 metre relay team and the other a bronze-medal winning weightlifter, adding that the B samples were due to be examined next week.
The minister said that the associations had not acted despite being notified of the results by the Olympic Council of Malaysia and threatened to step in if required.
"We need to resolve this issue as soon as possible but the fact that there has been no reaction from the associations is regrettable and embarrassing to the nation," he said.
"I am very sad this has happened and it is something we cannot tolerate.
"If they take this matter lightly, we can also take action. We must find out whether this is an isolated case involving an athlete or one which involves the whole association."
Malaysia won 59 gold, 50 silver and 81 bronze medals at the event.