Kenya's under 23 coach Leonard Saleh says he only learnt from the press the decision to withdraw from the All Africa Games.
The Kenyans were due to play Uganda this weekend in the return leg of the final qualifying round, having lost 5-1 in Nairobi.
Football Kenya Limited (FKL) said they could not afford to send the team to Kampala.
Saleh told BBC Sport he was not told of the decision before it was announced.
''I was very upset because I was responsible for the team, and I think I should have been the first person to be informed of the intention to withdraw.'' he said.
leh said the withdrawal was a setback for youth football in the country.
''It is not just about qualifying; we need to take part in these tournaments in order to develop a strong national team.''
He said he was confident that the team would have got a better result than in the first leg.
Uganda have qualified following Kenya's withdrawal.
Hosts Mozambique, Egypt and Madagascar have already qualified and the last four slots are to be decided this weekend.
Ghana host their bitter rivals Nigeria in Kumasi with the Black Meteors needing to overcome a 3-1 deficit from the first leg.
Ghana's preparations for the clash have been blighted by the uncertainty surrounding the availability of some key players.
Midfielder Emmanuel Agyemang Badu, Jonathan Mensah, Jordan Ayew and Richmond Boakye Yiadom remain doubtful for the crucial clash due to their involvement in pre-season training with their respective clubs in Europe.
After the first leg, Ghana's captain Samuel Inkoom told BBC Sport they were determined to overturn the deficit.
" I spoke to the players and told them it's not over until it's over."
"Ghana against Nigeria is like a derby game - they may have won but we are going back to Ghana to correct our mistakes.'' said Inkoom.
Nigeria have an advantage from the first leg win but an away goal will make things more comfortable for them, given that a 2-0 win for Ghana is enough to get them to Maputo.
They too have challenges with Ahmed Musa of VVV Venlo and Obiorah Nwankwo of Parma ruled out, but Austin Eguavoen's side has been boosted by the confirmation of two-goal hero in the first leg, Nosa Igiebor of Norwegian side Lillestrom.
Defending champions Cameroon, the most successful team in the history of All Africa Games, are in danger of missing out if they do not overcome a 1-0 deficit as they host DR Congo in Yaounde.
The Indomitable Cubs have already missed out on the 2012 Olympic Games in London.
South Africa will be taking a comfortable 2-0 lead to Zimbabwe , with alot expected from the on form Orlando Pirates' Bongani Ndulula, the scorer of the two first leg goals.
Senegal host Guinea in Dakar following a 1-0 defeat in Conakry two weeks ago.
The All Africa Games will take place from 3-18 September in Maputo, Mozambique.