The Shiv Sena party inked Sudheendra Kulkarni on Monday. Mr Kulkarni was organising the launch of a book by former Pakistani foreign minister Khurshid Mahmud Kasuri.
The party described the ink attack as a "peaceful protest" against Pakistan.
It later cancelled a planned protest at the launch of the book.
"We have arrested six men, they are all Shiv Sainiks and have been released on bail," Mumbai Police Deputy Commissioner Dhananjay Kulkarni told AFP news agency.
Sudheendra Kulkarni, who was admitted to hospital to have the ink removed, has condemned the incident as an "assault on democracy".
However the launch of Khurshid Mahmud Kasuri's book "Neither a Hawk nor a Dove: An Insider's Account of Pakistan's Foreign Policy" was carried out without incident after the party cancelled a planned protest at the launch.
The Shiv Sena party is a junior coalition partner in the Maharashtra state government, which is ruled by India's governing BJP.
The party was founded in 1966 to keep south Indian migrants out of Maharashtra state and to halt the spread of Islam.
Over time, it has acquired a reputation for promoting religious and ethnic chauvinism while allegedly targeting minorities, especially Muslims.
The Shiv Sena also forced the cancellation of a concert by Pakistani singer Ghulam Ali last week.
Pakistan has conveyed to India its concerns over the two recent incidents "in which Hindu extremist groups have interfered with gatherings involving Pakistani citizens," a foreign office spokesman has said.