Video posted on social networks showed a flash close to the fighter, which landed at Goma airport. AFP journalists in the eastern DRC city of Goma heard a loud explosion followed by two shots as the Congolese aircraft flew over Tuesday afternoon.
"A Sukhoi-25 fighter jet from the Democratic Republic of Congo violated for the third time Rwandan airspace," over Rubavu district, near Goma, Rwandan government spokesperson Yolande Makolo said in a statement.
"Defensive measures were taken," she said, adding, "Rwanda asks the DRC to stop this aggression."
The two previous cases were reported in November and December and saw protests from Kigali.
The DRC authorities had made no comment.
Kinshasa accuses Kigali of backing the M23 rebel group, which has captured swaths of Congolese territory in recent months. Kigali denies the allegations — which are backed by U.N. experts, the U.S., France and Belgium — in turn accusing Kinshasa of colluding with the FDLR, a former Rwandan Hutu rebel group based in the DRC.
The fighting between Congolese troops and the M23, which has made advances towards Goma, capital of North Kivu province, has prompted the East African Community (EAC) bloc to deploy a joint regional force to quell the violence.
Rwanda last week accused DRC of abandoning a deal aimed at restoring peace.
Talks between the DRC and Rwanda in the Angolan capital Luanda unlocked a truce agreement in November.
But last week the neighbors traded blame for continued fighting.
Scores of armed groups roam the mineral-rich eastern DRC, many a legacy of two regional wars at the end of the 20th century that claimed millions of lives.
The M23 first rose to prominence in 2012 and resumed fighting in late 2021 — claiming Kinshasa had failed to honor a pledge to integrate them into the army, among other grievances.