He has been indicted by the Sarkaria commission for corruption in allotting tenders for the Veeranam project.

The Interim report of Justice Jain Commission which oversaw the investigation into Rajiv Gandhi’s assassination indicted Karunanidhi for abetting the LTTE. The interim report, recommended that Tamil Nadu Chief Minister M. Karunanidhi and the DMK party be held responsible for abetting Rajiv Gandhi’s murderers. The final report contained no such allegations.

Karunanidhi has been accused by opponents, many of his party members and some political observers of trying to promote nepotism and start a political dynasty along the lines of the Nehru-Gandhi family. Vaiko who quit the DMK has been the most vocal. Political observers say that Vaiko was sidelined as he was seen as a threat to M.K.Stalin and other family members.

His nephew, the late Murasoli Maran was a Union Minister however it has been pointed out that he was in politics much before Karunanidhi became the Chief Minister in 1969.He was arrested several times including the Anti-Hindi agitations in 1965. He was asked to contest the by-election for South Madras in 1967 and the nomination papers were signed by Rajaji, Annadurai and Mohammed Ismail(Quaid-e-Milleth) clearly showing that his political career did not raise only due to Karunanidhi.

Many political opponents and DMK Party senior leaders have been critical and perturbed about the rise of M.K. Stalin in the party. But some of the party men have pointed out that M.K. Stalin has come up on his own. He has faced a lot of hardship since 1975 when he was jailed under MISA was beaten up in jail so brutally during the Emergency that fellow DMK Party prisoner died trying to save him. Stalin was a MLA in 1989 and 1996 when his father Karunanidhi was the Chief Minister but he was not inducted into the Cabinet. He contested and became Chennai’s 44 mayor but the first directly elected Mayor in 1996. It was only in his 4th term as MLA has he been made a Minister in the Karunanidhi cabinet and his rise is slow but steady.

Karunanidhi has been accused of helping Murasoli Maran’s son Kalanidhi Maran who runs Sun Network, India’s second largest television network and according to Forbes, Kalanidhi is among India’s Richest 20 with $1.9 Billion. Again commentators say that he raised himself into the position on his own merit and even Karunanidhi’s sons have achieved nothing compared to him which has been a cause of friction between them. His channels have been the mouth organ of the DMK party (until recent time) and balanced the Jaya TV of the AIADMK.

Another son of Maran’s, Dayanidhi Maran is a Former Union Minister for Communications & IT portfolio, not broadcasting ministry, which is responsible for TV networks. It is a well known and often-argued fact that Dayanidhi Maran has been thrown out of his IT and Communications portfolio at Center (he was a Union Minister for IT and Communications) because the Dinakaran Newspaper (run by the Maran brothers) has shown M.K. Stalin of having the possibility to be the next Chief Minister of Tamilnadu which created a bloody violence in the Madurai branch of Dinakaran office (carried out by M.K. Azhagiri), causing the death of three employees. This is again seen as a result of the Dynasty-Controversy in Karunanidhi’s family.

It has been pointed out that Karunanidhi has not hesitated to take action against his erring family members, Karunanidhi has even expelled his other sons MK Muthu and M.K. Azhagiri when they were guilty of wrong doing and similarly removed Dayanidhi Maran from the position of Union Minister (because of the reason stated in the previous paragraph).

But, he has been accused of not taking action against M.K. Azhagiri after his supporters attacked the newspaper office of Dinakaran killing 3 people (as stated above). M.K. Azhagiri is the prime accused in the murder case of the former DMK Minister Kiruttinan. Karunanidhi is also accused of allowing Azhagiri to function as an extra constitutional authority in Madurai through he has never held a party post and is a liabilty to the party and not yet expelled from the party. The Dinakaran newspaper case has been handed over to the CBI.

Further his daughter Kanimozhi has been nominated for a Rajya Sabha post even though she has done very little for the party as pointed out by critics and many of his party members.

In response to the recent Sethusamudram controversy, Karunanidhi questioned the existence of Rama. He asked

“ Some say there was a person over 17 lakh years ago. His name was Rama. Do not touch the bridge (Ramar Sethu) constructed by him. Who is this Rama? From which engineering college did he graduate? Is there any proof for this? ”

His remarks caused a firestorm of opinions. Tamil Nadu BJP head, Ravi Shankar Prasad accused Karunanidhi of religious discrimination when noting “We would like to know from Karunanidhi if he would make a similar statement against religious head of any other religion; chance are he may not.”

Nationalist Congress Party spokesman D. P. Tripathi said “Where is the need of asking for evidence on the existence of Ram when lots of people have unreserved faith in him?”

In response to these statements, Karunanidhi defiantly stated “Anyway, neither Valmiki nor Ram is here now (to vouch for claims of Ram’s existence). There is only a group that thinks of people as fools. They will be proved wrong.”

Few days later, he commented that Lord Rama was a drunkard

“ I have not said anything more than Valmiki, who authored Ramayana. Valmiki had even stated that Rama was a drunkard. Have I said so? ”

In late 2007, senior VHP leader and former BJP MP Ram Vilas Vedanti declared at a press conference that VHP saints of Ayodhya would weigh in gold anyone who beheaded Tamil Nadu Chief Minister Karunanidhi and cut out his tongue.

A lawyer has filed a petition in the Jharkhand High Court seeking a directive to register a criminal case M. Karunanidhi for his remarks against Ram.