Nisith Pramanik and Khagen Murmu were taken into custody to prevent any breach of law and order when they tried to go to Harishchandrapur and Bhaluka Road stations.
The duo were detained at Sukanta More soon after they started off for Harishchandrapur from Malda city.
The MPs tried to proceed by breaking through the police cordon but were stopped.
As BJP activists raised slogans and surrounded the police vehicles, the lawkeepers arrested the two MPs and took them to Englishbazar police station.
They were later released on bail, but not allowed to visit the two stations.
Pramanik later accused the administration of being partisan and said they would raise the issue in the Parliament.
"We had started off for Harishchandrapur. But the partisan police and administration has stopped our delegation midway as per prodding from the ruling Trinamool Congress.
"The state government is indirectly backing the perpetrators of violence. We will raise the matter in parliament," he said.
Earlier in the day, Chief Minister Mamata Banerjee alleged the two MPs wanted to go to the area to foment disturbances.
"What is the need for you to go there? What happened in Delhi. Who is stopping you there? Go to Lalbagh, Karolbagh, Amritsar, Bhagalpur.
"Whenever there is any incident, they stealthily get into it. But when the situation turns peaceful, then cat comes out of the bag. I won't allow any disturbance," she said.
Banerjee appealed to Union Home Minister Amit Shah to control his party and "control the country".
( With inputs from IANS )