Ibn Chambas, president of the 15-member regional bloc Ecowas, told the BBC's Network Africa programme that he was encouraged by the comments.
"The statement that the military has released indicates that they will stay out of the political affray and they have indicated what happened was not a coup d'etat, or even an attempted coup d'etat, it was a criminal act of assassination and I think there has been a very responsible position of the military," he said.
"We will urge them to continue to maintain this democratic, republican posture and accept civilian control to be the answer."
Moment of silence
Before taking the oath of office on Tuesday, national assembly leader Mr Pereira said Guinea-Bissau was "facing a very delicate situation".
He called on MPs "to assume their responsibility toward the nation".
"Since the era of democracy came to Guinea-Bissau, most presidents have been unable to finish their mandate," AP news agency quotes him as saying.
"My time in office will be temporary, but I will do my all to organise elections in time."
Lawmakers in the capital Bissau also observed a moment of silence for President Vieira and for the army chief-of-staff Gen Tagme Na Waie.
Soldiers killed President Vieira early on Monday in an apparent tit-for-tat attack after Gen Waie was blown up in his headquarters hours earlier.
Mr Chambas said the country would need financial and technical support to be able to conduct credible elections within 60 days.
"Ecowas will lead the way," he said.
"We will work to mobilise the international community, African Union, United Nations, the EU and others to be able to provide Guinea-Bissau with the resources that it needs to ensure that we have successful elections."
The UN Security Council said in a statement the 15-member body "condemns in the strongest terms the assassinations".
But the African Union's Peace and Security Council decided not to suspend Guinea-Bissau when it met in the Ethiopian capital Addis Ababa on Tuesday, as it said the attacks did not represent a coup.
The AU suspended neighbouring Guinea and Mauritania after coups last year.
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