Malawi's government says it will not hesitate to use soldiers to enforce Tuesday's deadline for all traders to leave the streets.
There was a huge growth in street vending in the 1990s
On Monday, police fired tear gas to disperse thousands of protesters.
As part of their protests the vendors were holding a prayer meeting, which the police said was unauthorised.
The BBC's Raphael Tenthani in the commercial capital, Blantyre, says there is a heavy police presence and no sign of vendors trying to resist.
The government says it is trying to restore order to Malawi's streets. The vendors say the designated markets are not suitable for them.
Abdul-Malik Kakowa, Vice-Secretary for the Limbe Street Vendors, told our correspondent the vendors did not want to move off the streets because the places authorities wanted them to trade from were not ideal for profitable trading.
"Imagine, they want us to move to a place like a rubbish dump, a bare garden... who is going to buy from us?" he said.
Mr Kakowa said the designated places also did not have running water and other sanitary facilities.
Local Government and Rural Development Minister George Chaponda said the government would go ahead with plans to evict the vendors from the streets in the country's city centres, despite the Blantyre riots.
"We want to bring sanity to our streets," he said.
Mr Chaponda said the government had spent millions of kwacha constructing flea markets for the vendors to trade from.
He said any vendor who did not leave the streets would be forcibly moved by the paramilitary police backed by army officers.
Monday's trouble started after negotiations and efforts to get a court order stopping the government from forcefully removing the vendors failed.
They decided to seek divine intervention and held noisy prayers outside Blantyre's main football stadium.
Willie Soko, officer-in-charge for Limbe, Blantyre's business district, told journalists police fires tear gas because the prayer meeting had not been authorised.
"They had no permission to conduct the prayers so we had to disperse them for fear of rioting," he said.
At least 30 vendors were arrested and charged with illegal assembly. Some braved the tear gas and held the prayers.
Street vending mushroomed in Malawi when the regime of former President Bakili Muluzi liberalised the economy in the early 1990s.
Mr Muluzi encouraged informal trading, saying it was part of his poverty eradication programme.