Early on Monday, heavy gunfire was heard at two military camps in Akouedo in the east of Abidjan, that together form the country's largest military barracks, a resident living nearby said.
Shots were also heard from Gallieni camp in the city centre.
Sustained gunfire rang out in Bouake, where one person died on Sunday from bullet wounds.
The situation was also tense in Man in the west and Bondoukou and Daloa in the centre of the country, where sporadic shooting could be heard.
The African Development Bank advised its employees in Abidjan to stay at home, warning that the security situation remained unclear.
Under a deal negotiated with the government in January following the initial protest, the ex-rebels were to be paid bonuses of 12 million CFA francs (18,000 euros) each.
They were given a partial payment of five million francs with the remainder to be paid starting this month, according to sources among the protesting soldiers.
But the government has struggled to pay the promised money.
Bouake served as the rebel headquarters following a failed coup in 2002 which split Ivory Coast in half and led to years of unrest.
The former star French colony has since been slowly regaining its credentials as a West African powerhouse and a haven of peace and prosperity.
But falling cocoa prices have hobbled the government's finances.
The current round of trouble began late Thursday when a soldier presented as a spokesman for the former rebels said they wished to apologise to Ouattara for the January mutiny and were renouncing their demand for huge payouts.
But the "apology", which was delivered in a televised ceremony, was viewed with scepticism by many of the mutinous soldiers.
Last year, the government unveiled a plan to modernise the military, part of which would involve the departure of several thousand men, mainly ex-rebels, who will not be replaced.