Additional district court directed the police to arrest the actor-politician and produce him before it before June 5.
The government advocate has filed the case accusing Vijaykanth of making defamatory remarks against Chief Minister Jayalalithaa during a public meeting at Palayamkottai here on August 6 last year.
The court had earlier issued notice to Vijaykanth directing him to appear today.
Terming the warrant as "unexpected", the party in a statement said Vijayakanth's urgent meeting with his party MLAs to discuss the issue of them not being allowed to initiate debates in the assembly was the reason for the non- appearance of their leader in the court.
It said Vijaykanth had no intention of disrespecting court orders.