Manchester City admitted that they forgot to tell Wales that the striker was injured and would not be available for Wednesday night's match in the Gradski Stadium.
Toshack flew to Podgorica with his squad on Monday without any idea what was wrong with Bellamy, and crucially not having had the opportunity to call up a replacement.
But Bellamy has phoned the team hotel here, clearly upset with the situation and, it is understood, has made it clear that his track record of being available for his country is beyond reproach.
Bellamy is 'far from impressed' that his club failed to inform the FA of Wales that he was not going to make the trip.
And he feels that he has been 'hung out to dry' over the situation, having suffered a reaction to his knee problem after scoring the winner for City on Saturday in their friendly with Celtic at Eastlands.
Toshack was careful not to inflame an already difficult situation with Mark Hughes, his predecessor as Wales manager, and unconditionally accepted Bellamy's explanation.
The FAW are mindful that it was Bellamy's frantic calls to the team hotel here that defused a worrying situation.
One Wales source pointed out: "Can you imagine the uproar had this been John Terry not turning up for England, and Chelsea not telling the English FA before the team flew out for a match?"
Toshack named Cardiff's Joe Ledley as captain for tomorrow's game, and it is clear that Bellamy's position in the squad is not in question.
Toshack, though, was not impressed with the saga that dogged him for 48 hours before he arrived in the Montenegro capital.
He said: "Craig has been in touch with us at the team hotel. Manchester City's statement is self-explanatory.
"We have to accept that. There seems to have been some misunderstanding from within the club there, and the text messages that we have received underline that.
"Now we have a game to play, we want to concentrate on that. Apart from Craig's withdrawal we lost four other players from the squad.
"David Vaughan rang me and said he had a family problem to resolve (over his wife's pregnancy) so that was understandable.
"Phil Brown (Hull manager) rang me to tell me that Boaz Myhill had a wrist injury, and Carl Fletcher has retired.
"He spoke to me on Sunday about that, I would have preferred to have known a bit earlier because we were not able to get a replacement sorted out.
"He explained his reasons and I understand that. He has seen the thread of young players coming through in midfield and he has called it a day.
"David Edwards travelled down from the Midlands to see our medical people over his groin injury, and it was clear he was in some discomfort and he was sent straight back to Wolves.
"But we have a decent balance in the squad still, and we are looking forward now to carrying on the good work that we started with the excellent win in Azerbaijan in our last match."
Toshack added: "We have seen what Manchester City have said, but I want to concentrate on our match here. That is vital in our build-up for the next World Cup qualifier with Russia.
On the fact that Bellamy failed to call the Wales HQ himself on Sunday, Toshack said: "All players are different. We have to accept that the lines got crossed between the player and City.
"We got the information a little bit later than we would have liked, to be honest.
"It is understandable we would have liked to have heard a bit earlier, but you have to accept the explanation that has been given to us.
"We would like to think we would have been notified a bit earlier than we were, it was just an accident. We need to concentrate on the game now."
Wales have won their last two matches, and Toshack desperately wants to build on the feelgood factor that followed the impressive win in Azerbaijan last season, with a team a young players.
Toshack said: "When I started this job almost six years ago, several of the lads who will be playing against Montenegro were still at school. That underlines how far we have come and what has been achieved with young players."
He added: "There are a lot of positive signs. We have Danny Gabbidon back after almost two years out through injury and we are delighted with that.
"There were times when we felt we would not see him again, so it is a really boost to have him available. The same applies to James Collins, who has not always been that reliable due to injuries. They are both here and that is a tremendous bonus for us."
Toshack did not go as far as to say Bellamy will retain the captaincy, but did add: "Joe Ledley will be captain against Montenegro. He has done the job for the last couple of games, so we will leave it at that for the time being."