The shootings - just days before a visit by US President George Bush - is causing the government a huge political and domestic headache.
The bodies of three shot protesters were shown on Nigerian television on Monday which erupted into a day of protest across the country, but union chiefs said the number of dead was at least 10.
Police officials declined to comment until further investigations into the shootings are carried out.
Oil shipments from Nigeria, the world’s eighth largest exporter, are again under threat because of the two-week strike, the worst-ever in living memory.
Scores of fires were burning in the industrial and impoverished sector of Lagos as protesters became more militant.
“These are rioters. We are trying to deal with the situation,” said Nibo Komonibo, the city’s deputy police commissioner in charge of operations.
In the mainly industrial district of Oshodi, hundreds of frightened people were stranded at bus stops. Youths chanted slogans critical of President Olusegun Obasanjo.
Hopes for a deal between the government and labour unions to end Nigeria’s longest strike in four decades were unexpectedly dashed on Sunday over a gap of less than three US cents between them on the price of a litre of petrol.
The Nigeria Labour Congress (NLC) said the strike it launched on 30 June would continue until Obasanjo agreed to lower the price from 35 Naira (27 US cents) a litre to 32 Naira.
NLC President, Adams Oshiomhole, told a news conference the umbrella group’s policy-making executive body had rejected the price and urged the NLC to mobilise other campaign groups to make the strike bite even harder.
Nigeria's umbrella labour union
urged other groups to join
The strike has already shut ports, shops and banks. Nigerians also report phone failures, and power workers say supplies cannot be guaranteed from Tuesday.
In the first week of the strike, police killed at least five protesters and fired hundreds of tear gas grenades.
The strike was triggered when Obasanjo announced an increase of more than 50% in petrol prices last month, on the grounds that it was essential for Nigeria’s economy to reduce subsidies on imported refined fuel.
Nigeria’s own refineries cannot meet domestic demand, so the OPEC member has to import to meet the shortfall.
Obasanjo, whose re-election in April sparked opposition accusations of vote-rigging, now faces mounting pressure from economic disruption and the prospect of wider political protests.