Police intercepted Mr Stalin's convoy of vehicles and detained him at a check post in Kaniyur after he insisted on proceeding to Salem, police said.
Talking to reporters from his car, the Leader of Opposition in the state Assembly claimed that the police denied him permission to visit Salem to participate in the human chain protest seeking exemption for the state from NEET.
Though there was no ban on him visiting the lake, police barred him from going there as well, citing law and order problem, he said.
Besides Mr Stalin, several other DMK workers were arrested, they said.
"This is nothing but an effort to defame DMK, which with the support of other parties has taken up the students' cause over NEET and is organising the human chain," he alleged.
A large number of DMK workers gathered at the check post on the National Highway, and raised slogans against the state government and police over the arrest of their leader.
Mr Stalin had earlier appealed to the cadres not to get agitated and court arrest, since they were needed to take part in the human chain protest for the benefit of Tamil Nadu students.
Yesterday, over 800 DMK workers were arrested from various parts of this district for staging road rokos protesting the desilting of the Katcharayan lake in Chief Minister EK Palaniswami's constituency, by farmers owing allegiance to ruling AIADMK (Amma) allegedly using earth movers.
DMK workers said they had desilted part of the lake and strengthened its bunds together with some farmers.
But farmers belonging to ruling AIADMK had removed the silt by using earth movers, resulting in damage to the bunds, they had alleged.
Workers of the rival parties had on July 25 clashed over the issue, forcing the administration to stop the desilting work for a day.