Junctions three, at Swanley in Kent, nine at Leatherhead in Surrey, and 28, near Brentwood in Essex, were targeted on Friday morning. Surrey Police said officers had arrested 14 people at junction nine.
Members of Insulate Britain also converged on junction one of the M3 as part of their coordinated demonstrations against climate change - with Home Secretary Priti Patel attacking their “guerrilla tactics”.
Transport Secretary Grant Shapps urged Surrey and Kent Police to take "swift action" to stop the "dangerous and counterproductive" protests.
The senior minister said: "We all agree that climate change must be tackled, but this sort of behaviour achieves nothing, puts drivers at risk and increases pollution. I expect the police to take swift action to clear the roads.”
Insulate Britain claimed 79 people attempted to block the London orbital motorway hours after their release from police custody following similar protests earlier this week.
It comes as the Home Secretary Priti Patel is said to have called on police to crack down on the protests which brought traffic to a halt.
Surrey Police said on Friday: “We were made aware of protesters at junction 9 of the M25 earlier this morning. 14 people have been arrested. We were also made aware shortly after 9am of protesters at junction 1 of the M3. We are on the scene and arrests are being made. Further updates to follow.”
The force added that 10 arrests were made on the M3, with both roads now clear.
Ms Patel had already criticised the “selfish” protesters, some of whom had glued themselves to the road, after they stopped thousands of motorists at four junctions on Britain’s busiest motorway shortly after 8am on Wednesday for the second time in three days.
She said the “guerrilla tactics” used by the protesters “detract from their cause” and, although insisting there will “always be space for legitimate groups to make their voices heard”, added: “This Government will not stand by and allow a small minority of selfish protesters to cause significant disruption to the lives and livelihoods of the hard-working majority.”
Insulate Britain said its “actions will continue until the Government makes a meaningful commitment to insulate all of Britain’s 29 million leaky homes by 2030, which are among the oldest and most energy inefficient in Europe.”