The UEFA Nations League match between Romania and Kosovo was suspended in stoppage time with the score 0-0 in Bucharest on Friday.
There were scuffles between players from both teams and Kosovo players walked off the pitch.
UEFA did not explain why the game was cut short but Kosovo players were reportedly upset at hearing pro-Serbian slogans. In a note on its website [posted Friday, UEFA said that the game had been "abandoned" and that it would "communicate further information in due course."
On Saturday, the governing body said disciplinary proceedings have been instigated against both federations.
After historic tensions were heightened by the 1990s Balkans conflicts, in 2008 majority ethnic Albanians in Kosovo declared independence for the former Serbian province. Serbia refuses to recognize that independence and considers Kosovo the cradle of its statehood.
Games involving Kosovo, Albania and Serbia have been a tinder box in recent years.
The Kosovan Football Federation (FFK) released a statement saying they had repeatedly told UEFA that the match could be affected by the tensions.
"Cries such as 'Kosovo is Serbia' and 'Serbia, Serbia', whistling during the singing of the national anthem of Kosovo, throwing hard objects ... and other offensive and provocative actions were present throughout the match, creating an unacceptable atmosphere not safe for our players," the FFK statement said.
"FFK had warned the relevant UEFA bodies more than twice in writing about the possibility of such actions, once a few days before the match and then a few minutes before it started.
"Despite these warnings, the Romanian fans continued with irresponsible and discriminatory behaviour, forcing the Kosovo national team to leave the field due to the lack of safety and dignity.
"For all these serious violations, FFK has immediately reported the incidents to the match delegate and has started preparing a full complaint with facts and evidence that will be submitted to UEFA's disciplinary bodies," it added.
The Romanian Football Federation (FRF) responded with a statement of their own on Saturday which said it was disappointed by the behaviour of the Kosovo delegation and players, describing their accusations as baseless while also saying their actions were premeditated.
"It is important to emphasise that there were no racist chants during the match, nor was the slogan 'Kosovo is Serbia' chanted even once," the FRF said.
"Moreover, we would like to remind everyone of the decision made by UEFA's Disciplinary Committee regarding a similar incident during a match last year, where Kosovo acted in the same manner.
"The decision clearly stated that the slogan 'Kosovo is Serbia' cannot be classified as racist and, therefore, cannot trigger the three-step procedure."
Information from Reuters and The Associated Press contributed to this report.