Nigerian President Paula Tinubu's spokesman said on Thursday that the president directed that disputes with Emirates Airlines and an issue related to the UAE's issuance of visas be resolved immediately.
The UAE stopped issuing visas to Nigerians last year after Emirates Airlines in Dubai grounded its flights because it could not get its money from Africa's largest economy.
Tinubu's office said in a statement on Thursday that it had met with the UAE's ambassador to Nigeria, Salim Saeed Al Shamsi, and that Tinubu was ready to intervene "personally" in the dispute.
"We have to work together. We have to agree on basic aviation and immigration issues," Tinubu said in the statement.
"We have reached something. These are small issues, all within the family, and they will find their way to a solution," the statement quoted Al Shamsi as saying.
Emirates said in March it had "significant" proceeds withheld in Nigeria and had made slow progress in obtaining the withheld funds.
The International Air Transport Association (IATA) said in March that Nigeria was withholding at least $743 million in revenue earned by international airlines operating in the country.
Nigeria, Africa's largest oil producer, is facing a shortage of foreign exchange despite some reforms.