A government source in the Macedonian capital Skopje said on Thursday all nine people on board the small plane died when it went down near the town of Stolac, in the early hours of Thursday morning.
In addition to Trajkovski, the dead were identified as chief press officer Dimka Ilkova Boskovic, advisors Risto Blazevski and Anita Lozanovska, foreign affairs ministry official Mile Krstevski and security officers Ace Bozinovski and Boris Velinovski.
The co-pilot was identified as Branko Ivanovski but the name of the pilot was not immediately known.
Bosnian radio reported that the wreckage of the plane was found in southern Bosnia and there were no survivors.
Boris Trajkovski, whose tenure was marked by the 2001 crisis with ethnic Albanian rebels that brought the former Yugoslav republic to the brink of civil war, had been on a short flight to the Bosnian city of Mostar for an economic conference.
An official in Skopje said the plane went down "somewhere near Stolac", a zone of treacherous winter skies for aviation amid mountains east and north of Croatia's Adriatic port of Dubrovnik.
"At about nine o'clock this morning, the radar lost control of an aircraft," said Zoran Glusac, a spokesman for the Bosnian Serb interior ministry. Local police reported an explosion in the mountains between Stolac and the village of Ljubinje.
"The weather conditions were very bad with heavy fog and rain," Glusac said. Police were sent to the crash site on Hrgut mountain. The US-led NATO peacekeeping force in Bosnia, which has helicopters, said it was on standby in case help was requested.
"At about nine o'clock this morning, the radar lost control of an aircraft. Local police reported an explosion in the mountains between Stolac and the village of Ljubinje. The weather conditions were very bad with heavy fog and rain"
PM to return
Macedonian Prime Minister Branko Crvenkovski was in Dublin when news of the crash was announced, on a mission to formally deliver his country's application to join the European
Union, of which Ireland hold the presidency at the moment.
Journalists travelling with him were told to pack up and be ready for an immediate flight back to Macedonia.
The mountainous Balkan region, combined with difficult winter weather conditions, can be hazardous for air travel.
In April 1996, a member of US President Bill Clinton's cabinet, Commerce Secretary Ron Brown, was among 35 people killed when a US Air Force passenger jet crashed into a mountain in the same area.
From his election in late 1999, Trajkovski's term was marked
by tensions between Slavic-speaking Macedonians and the former Yugoslav republic's large ethnic Albanian minority.
Although his powers were limited and his role largely ceremonial, he presided over a NATO-brokered peace deal in 2001 that ended months of armed clashes and prevented a full blown civil war in the mountainous state bordering Kosovo.
Trajkovski was married with a son and a daughter and was viewed in the West as a young leader with an international outlook and an ability to build contacts abroad.