The yatra, set to begin from the banks of River Saryu, had earlier been banned by the Akhilesh Yadav government.
While Mahant Nritya Gopal Das was detained with 100 supporters and followers after he set out from his ashram for Saryu Pujan, marking the beginning of the yatra, Pravin Togadia was arrested from outside the Satguru Sharan temple.
Police had a tough time as supporters of the VHP leader raised anti-government slogans and tried to prevent the police from whisking Togadia away.
Senior VHP leader Ashok Singhal was arrested at the Chowdhary Charan Singh Amausi international airport in Lucknow, and was not even allowed to come out of the airport.
The district officials told him that he cannot proceed towards Ayodhya. Officials told IANS that the state government had instructed police officials to arrest him at the airport and ask him to fly back to New Delhi by the 1 p.m. flight.
Togadia, meanwhile, told reporters that the state government was depriving the community of ascetics their basic religious rights by clamping down on the proposed yatra.
"The state government has made a political issue out of something entirely non-political, and this is being done to appease a particular community," Togadia said.
Even though a heavy police posse was present at vantage points in Ayodhya, over two dozen VHP workers and a group of four seers did manage to give them a slip, taking a bath at the Saryu river and performing "Saryu Puja".
They were later arrested and taken to an undisclosed destination.
A home department official said more than 500 religious men and VHP workers had been arrested across the state as they were trying to travel to Ayodhya.
The Akhilesh Yadav government had last week banned the proposed ritual, citing fears that it would disturb communal harmony in the state.
The Lucknow bench of the Allahabad High Court (HC) had Saturday dismissed a petition against the ban on the yatra, being held in support of the Ram Mandir at the disputed site.