Emirates said it had made no progress in efforts to initiate dialogue with the relevant authorities for their urgent intervention.
"Therefore, Emirates has taken the difficult decision to suspend all flights to and from Nigeria, effective 1 September 2022, to limit further losses and impact on our operational costs that continue to accumulate in the market," it said in a statement.
A Federal Ministry of Aviation spokesperson did not immediately respond to a request for comment.
The decision highlights the difficulties faced by international carriers that fly to Nigeria, which is one of the biggest markets on the continent for several of them.
The country has restricted access to foreign currency for imports and for investors seeking to repatriate their profits due to a shortage of dollars. Nigeria gets about 90% of its foreign exchange from oil, but is struggling to produce due to pipeline theft and years of under-investment.
The International Air Transport Association said in June Nigeria was withholding $450 million in revenue that international carriers operating in the country had earned.
Emirates said it would re-evaluate its decision if the situation over the blocked funds changed in the coming days. Affected customers would be helped to make alternative travel arrangements where possible, it added.