This month's 2022 FIFA World Cup qualifying match between Spain and Kosovo will be played in accordance withvFIFA and UEFA rules.
Kosovo's football federation (FFK) had stated that it would not play the March 31 fixture in Seville unless Spain pledged to respect the country's sovereignty, flag, and national anthem.
Spain does not recognise Kosovo's declaration of independence from Serbia in 2008.
The FKK had taken issue with references made on Twitter by Spain's national football team (RFEF) that described Kosovo as a "territory".
"The approach of the Spanish state towards the state of Kosovo has unfortunately been destructive," the association said in a statement.
"The attempt of the Spaniards to minimize the statehood of Kosovo ... is in vain and unfair."
But on Wednesday, the head of the FFK, Agim Ademi, said he had spoken with officials from Spain's football association to resolve the matter.
"RFEF expressed regret for the news published in the local media and confirmed that the Spain-Kosovo match will take place in accordance with the regulations and protocol of FIFA and UEFA for official matches," a statement said.
"Also, the Spanish Football Federation has expressed their hospitality for the Kosovo National Team and was open in cooperation for any need that FFK may have."
Ademi added that UEFA had also given the same assurances and confirmed that the match would go ahead as planned with Kosovo's national emblems.
Kosovo and Spain are paired in Group B together with Sweden, Greece, and Georgia, to qualify for the 2022 tournament in Qatar. The latter two countries also do not recognise Kosovo as an independent nation.
Most other western nations have recognised Kosovo's independence, and the country became a UEFA and FIFA member in 2016.
The FFK had warned that Spain's earlier actions would damage relations between the countries and federations.
"We shall ask for protection ... as we are a UEFA member with equal rights like the 54 other federations and Spain is obliged to treat us like that," it said.
Two years ago, Spain's refusal to respect the flag and anthem of Kosovo forced UEFA to move qualifying games for the under-17 European Championship.
But the President of Spain's government council for sports (CSD) has said that there is "not the slightest problem".
"The conditions in which the match is going to take place are absolutely normal," Irene Lozano told the Senate on Thursday.
"It does not imply a political recognition of Kosovo, because it is Spain's position and it is not going to change because of a match".
"That is one of the great virtues of sport, to be able to overcome disputes of other kinds," Lozano added.