Emirates plans to cut the number of flights to Lagos to seven from 11 by mid-August, the letter said, adding it had $85 million stuck in the country as of July, a figure that had been rising by $10 million per month.
Emirates, in an emailed statement, said trouble repatriating funds was impacting its commercial viability in Nigeria and that efforts to solve the problem had been met with limited success.
"We have no choice but to take this action, to mitigate the continued losses Emirates is experiencing as a result of funds being blocked in Nigeria," it said in a letter to aviation minister Hadi Sirika dated July 22.
Emirates did not comment directly on the letter.
A spokesperson for the aviation ministry did not reply to a request for comment.
The International Air Transport Association said in June Nigeria was withholding hundreds of millions in revenue that international carriers operating in the country had earned.
Amid similar foreign exchange restrictions in 2016, several airlines reduced flights and carriers Iberia and United Airlines stopped flying to Nigeria altogether. The latter re-launched a Nigerian service last year, but Iberia has yet to return.