The government announced on Wednesday that the price was to increase in a bid to ease crippling fuel shortages.
The Nigeria Labour Congress (NLC) said the rise from 86.5 naira ($0.43) a litre to 145 naira should be reversed.
In 2012, the government was forced to back down on a similar price rise after nationwide protests.
The subsidy, which has kept the price low, costs the government $2.7m a day and there is no provision for it in the recently approved budget for this year, the petroleum ministry said in a statement.
Recent fuel shortages have seen Nigerians paying up to 350 naira a litre on the black market, it added.
Despite being one of Africa's largest oil producers, Nigeria has to import fuel to meet demand as its refineries are dilapidated and work at a fraction of their capacity.
Petroleum Minister Emmanuel Ibe Kachikwu said that the price rise should stabilise the market and help end the fuel scarcity.
But "even with the new price regime, Nigeria would remain one of the cheapest fuel markets in Africa," he added.
Some fuel stations in Nigeria have already begun to sell petrol at prices dictated by the market.
Many here in the capital, Abuja, started last night after the announcement that the subsidy had been scrapped.
Only filling stations owned by the state-run NNPC firm are selling at the old price until they exhaust their current stock.
And fuel is likely to be even more expensive in northern Nigeria because of the cost of transporting it there.
Related stories: Nigeria to fully deregulate petrol