The government had ordered security forces to do whatever was necessary to stop the protests in Kathmandu.
Kofi Annan, the UN secretary-general, has criticised the government clampdown, saying that citizens had the right to protest peacefully.
Meanwhile, communist rebels took 28 hostages during a raid in a town in the south of the country that left 13 people dead.
An opposition leader said around 300 people had been arrested whilst home ministry officials confirmed only 177.
Khadga Prasad Oli, a protest leader, said at least 16 demonstrations had taken place in Kathmandu and that they would resume on Friday morning.
Governdra Pandey, a home ministry spokesman, said:
"They threw stones at policemen and at cars, damaging eight vehicles. They burned tyres and broke the prohibitory orders."
King Gyanendra seized power
But he said that "the situation is quite normal. There is no law and order problem."
Oli said some of those arrested in Kathmandu had been sentenced to three months in prison under emergency laws and that others were being held without charge.
The rebels had pledged to suspend attacks in Kathmandu for the duration of the strike, but have continued their campaign outside the capital.
On Wednesday in the southern town of Malangawa, rebels bombed government buildings and raided security bases. They took 27 policemen and a local official hostage.
Six policemen, five rebels and two civilians died in the raid.
A government helicopter also crashed during the fighting, which rebels said they had shot down.
Annan criticised the government crackdown in a statement released through his spokesman, Stephane Dujarric.
"While maintenance of law and order is the responsibility of the state, security considerations should not be the basis for denying citizens their right to peaceful protest - a right for which virtually all avenues seem to be closing," Dujarric said.
Nepal sank into deeper political turmoil after King Gyanendra sacked the government and seized power in February last year.
The king says that he took power because of the growing insurgency, which has killed around 13,000 people since 1996.