"He (Modi) is not a good administrator," Mr Thomas said in a statement, a day after he reportedly mentioned at a function here that he was comfortable with the Prime Minister, an able administrator who could convince others about his decisions.
"What I said was... many of his (Modi's) administrative decisions like demonetisation, GST have gone wrong, but he was able to manage (the situation) with his management skills," the former Union minister said.
Mr Thomas, the former chairman of the Public Accounts Committee of Parliament, alleged that PM Modi, using his management skills, was able to manage the media and even the judiciary.
"That is a bad situation," he said.
Addressing the National Management convention in Kochi, Mr Thomas had reportedly said that regardless of whether his decisions were right or wrong, PM Modi was able to do it.
Talking to reporters in Kochi, the Congress lawmaker slammed the BJP-led central government for the disruptions witnessed in the second half of the Budget Session of Parliament, calling it a "government-sponsored stalling".
"In the second half of the Budget Session, it was the government that persuaded and managed the stalling of the House, using its allies on different issues like Andhra Pradesh and Tamil Nadu," he alleged.
Mr Thomas also described the Prime Minister's day-long fast on Thursday against parliament disruptions as a "drama".
The government did not want any discussion on the burning issues facing the country, including farmers' suicide and atrocities against women, he alleged.