The legislator was protesting under the banner of River Princess Hatao Manch, demanding removal of a huge cargo ship, which has run aground on north Goa's Candolim shore.
"Fernandes was arrested under 151 of CrPc as they had no permission to hold morcha in the city," sub divisional magistrate Sabhaji Shetye told media persons.
He said that the protestors were arrested to avoid problems at the Republic Day parade.
River Princess Hatao Manch, a non-government organisation, has began agitation in the state demanding removal of the ship, which has feared to become an ecological disaster.
The protestors were arrested at Panaji's Ferry Wharf, almost two kilometers away from the Republic Day function, when they were walking with placards in hand. The Republic Day function was attended by Goa Governor SS Sidhu, Chief Minister Digamber Kamat and other dignitaries.
Fernandes told PTI that they had no intention to sabotage the republic day parade.
"We would have sat peacefully at the parade with placards in hand. This was a peaceful silent protest," the legislator representing Calangute constituency said.
He said that 12 of the leaders were forcefully dumped into the bus by police and later all other protestors courted arrest.
Demanding that the state government immediately get rid of the cargo ship, which has been haunting them for the last eight years, Fernandes said that there will be lot of surprises in terms of agitation.
The legislator said that they had sought permission to hold the morcha, which was rejected on Sunday night.