The swift response indicated that the Kyrgyz government would not tolerate street actions pledged by the opposition, which has alleged massive fraud in the Bakiyev's landslide victory last week.
It was also the latest episode in a long history of political unrest in the volatile Central Asian state, an impoverished ex-Soviet republic home to a key US military base.
Opposition leaders blasted the government's "mediaeval" methods and urged the international community to intervene, in a letter posted on the website of Almazbek Atambayev, the main opposition candidate in last week's election.
"Bakiyev's family clan wants to force all poeple of Kyrgyzstan to their knees," said the letter, which was addressed to the United Nations, the European Commission and other international organisations.
World leaders should "influence the Kyrgyz authorities with the goal of forcing a swift end to all the repressions and freeing all the unlawfully arrested activists... and carrying out repeat elections," the letter said.
After the mass arrests, the opposition headquarters announced it was ending protests for the day and would resume them Thursday.
At least 150 protestors were arrested in Bishkek, said Alexandra Yakhnova, an activist in the opposition headquarters. However the Kyrgyz interior ministry confirmed only 43 arrests.
There were also reports of protests and arrests in other regions.
At one protest in Bishkek, scores of opposition supporters shouted slogans such as "Return the stolen power!" and were about to march on the presidental palace when police moved in, an AFP journalist witnessed.
Protestors were dragged away into buses. Police also attempted to detain the AFP journalist, apparently confusing her for one of the protestors.
The opposition later said that many people in the march had turned out to be plainclothes police masquerading as demonstrators who helped authorities arrest protestors.
Officials justified the arrests by saying the protestors had not obtained permission to demonstrate.
"Those people detained in Bishkek today violated the established order for organizing meetings, protests, street marches and demonstrations," interior ministry spokesman Bakyt Seitov told AFP.
The detained protestors would face penalties ranging from fines to 15 days in jail, Seitov said.
Incumbent president Bakiyev won the election with 76.43 percent of the vote compared to 8.39 percent for Atambayev, according to official results which are disputed by the opposition.
Western observers from the Organization for Cooperation and Security in Europe also criticised the election, citing widespread irregularites.
Kyrgyzstan has a history of political unrest. Bakiyev himself came to power after a 2005 popular uprising that ousted his predecessor, Askar Akayev.
Ironically, one of the key events in the 2005 uprising -- widely known as the "Tulip Revolution" -- was the storming by protestors of the presidential palace, the destination of Wednesday's abortive protest march.
Kyrgyzstan has been frequently criticised in the West for its record on democracy and human rights, but it is nonetheless seen as being more pluralistic than its Central Asian neighbours.
A mountainous country that borders the troubled Xinjiang region of China, Kyrgyzstan is home to a US airbase used to support operations in Afghanistan, as well as a nearby Russian military base.
Bakiyev came to international attention this year when he ordered the US airbase to shut down and then changed course after Washington agreed to pay millions of dollars more in rent.