Protesters threw pavement cement blocks, glass marble pebbles and water mixed with chillies at security forces late last night.
After a confrontation for over two hours, protesters were dispersed and roads were evacuated at around 1 am local time, Maldives police said.
More than 100 supporters has been arrested by police, Maldivian Democratic Party claimed at a press conference here.
MDP members had vowed that they will go on with these protests until the government of Mohamed Waheed was removed from power and presidential election were declared.
"MDP should understand that government cannot be toppled from the streets," President Waheed said after opening the Dialysis Unit at a Hospital in HulhuMale's island today.
MDP Spokesperson Imthiyaz 'Inthi' Fahmy vowed to continue with the protest and added that a protest will be organised in Colombo this Sunday.
Fahmy also said MDP was going to withdraw Nasheed's statement regarding the former President Maumoon, alleging that he was behind the coup.
Nasheed had resigned on February 7 this year in what he termed was a "coup" and was replaced by his then Vice President Waheed.