The kingdom's Interior Minister Prince Nayef bin Abd al-Aziz told a news conference overnight on Tuesday that the protest was staged by "some people who had been duped by others" - a reference to foreign dissidents.
It was not clear if those detained were still being held on Wednesday.
One person arrested on Tuesday said many of those arrested were released after a few hours.
Saudi Arabia tried to downplay rare protests by young Saudis demanding release of political prisoners and drastic reforms.
Prince Nayef said the demonstration was limited to 150 people carrying banners on women's rights.
"They were a small number. And thank God, millions of Saudi youth will not buy into what was said or (rumours) mentioned," he said.
Those involved had been arrested and were being questioned, said the interior minister.
Baton-wielding anti-riot police intervened to disperse hundreds of protesters after the London-based Movement for Islamic
Reform called for the rally against the detention of government opponents.
The opposition group timed the protest to coincide with a human rights conference that opened in Riyadh on Monday, the first such gathering in Saudi Arabia.
"We hope this will not be repeated in future," said Prince Nayef.
Protests are banned in Riyadh
Witnesses said police fired shots in the air and arrested about 50 people as 200 protesters marched through the capital to demand faster reforms in the absolute monarchy.
The kingdom has mounted sweeping arrests against Islamist dissidents, especially after bombings in Riyadh in May which killed 35 people.
The marchers, mostly under the age of 30, had disregarded a warning by Prince Nayef on Monday that protests were banned.
Instead, they appeared to have responded to calls by an exiled opposition group for vigils to highlight domestic issues such as unemployment, estimated at 12%, and crackdowns on reformists.
Saudi Arabia, facing international criticism over its harsh human rights record, is joining a regional trend towards cautious experiments with liberalisation.
It is under pressure at home and abroad to grant more freedoms and quash Islamist activists.
Riyadh has pledged more reforms, including improving job opportunities for women. On Monday the cabinet approved the country's first polls which will elect municipal councils.
The government has not said who will be eligible to vote, but women still cannot drive or travel without a male companion.