Private fuel distributors insisted that they were ready to cut prices by around a fifth after President Olusegun Obasanjo's government bowed to labour pressure and told them to comply with a court order to lower their rates.
But Adams Oshiomhole, leader of the Nigerian Labour Congress (NLC), said that the prices had not yet been brought down all across Nigeria, and in some cases had not fallen far enough.
"Because of this I regret to announce that the strike will continue," he told reporters in Abuja.
"It's only in Abuja that they've complied," he said, calling on government's Department of Petroleum Resources to enforce a February court order which froze prices when they varied between 39.5 and 44 naira per litre (30 cents).
Since February, private firms have ratcheted up prices to around 52 naira per litre, triggering a nationwide outburst of anger which culminated in Wednesday's launch by the NLC and other union groups of a general strike.
On Thursday, mobs of union activists toured station forecourts in Lagos and Abuja checking on prices and intimidating staff.
"If you sell at more than 38 naira per litre you will be in trouble," NLC vice-president Henry Adekwe warned staff at one Abuja petrol station as he led a large convoy of supporters around the city.
Meanwhile, the managing director of the Nigerian National Petroleum Corporation, a state-owned oil firm which also has a regulatory role, Funsho Kupolokun said it had warned private fuel firms to heed the court order.
"Any petrol station that refuses to comply will face the consequence. And what do I mean by this? The station gets sealed up," said Funsho Kupolokun, in an interview of state television. "The NNPC has complied and is complying."
Compared to a similar general strike almost exactly a year ago -- during which riots erupted and police killed around a dozen protesters -- the action was largely peaceful.
In Abuja union militants claimed that a motorcycle-taxi rider had been shot and wounded by police, and in Lagos street toughs demanded an impromptu strike tax from motorists, but there were no reports of large-scale unrest.
Both cities were busier than on the first day of the strike, but most banks, markets and government offices remained shut.
Nigerian fuel prices are still low by world standards but over the past year the oil-rich country, whose impoverished citizens traditionally regard cheap, subsidised fuel as a birthright, has seen a series of steep price hikes.
Obasanjo's government abolished subsidies and price controls on fuel in June last year as part of a programme of liberal economic reforms designed to halt Nigeria's seemingly inexorable slide into poverty.
But following last year's general strike the state has again taken a hand in controlling prices through an industry stakeholders' committee.
Private marketers say, however, that if forced to respect a rate of 38 naira per litre they cannot make a profit selling fuel which they have paid for on the international market and imported themselves.
"Government has directed that we reverse our prices. At the moment, we are in the process of reverting them. It is proper for the same government to ensure that we have a profit margin," said Total spokesman Tayo Akpata.
"Business is run for profit. We have listened to the government order. We are certain that the government which asked us to bring down our prices will find a way for us to make some profit on our business," he said.
The firms say that if they have to sell at 39 naira they will be forced to buy from the NNPC's limited stocks of subsidised petrol, which would mark an effective end to Obasanjo's deregulation policy and lead to fuel shortages.
Despite being Africa's largest crude oil exporter, Nigeria imports most of the refined fuel used by its 130-million-strong population, as corruption and incompetence have rendered its own oil refineries fatally inefficient.
