After toppling sitting president Umaro Sissoco Embalo on November 26, the junta originally alleged drug barons were conspiring to sow chaos in the country, a hotspot of cocaine-trafficking.
But on Thursday, in a document proclaiming the establishment of a consultative National Transitional Council, the authorities argued instead that the unstable country faced a "grave" political situation in the wake of the ballot "which could degenerate into a civil war with ethnic undertones".
"The Armed Forces were once again compelled to intervene, resulting in another change to the constitutional order through force," said a resolution issued by the junta's high military command on Thursday seen by AFP.
Guinea-Bissau had already seen four coups and numerous more attempted takeovers since independence from Portugal in 1974.
Opposition figures and analysts have suggested that last month's coup was carried out with Embalo's blessing to halt the electoral process.
The junta named General Horta N'Tam, considered a close ally of the president, to head a transitional administration set to last a year.
Embalo's main rival in the ballot, Fernando Dias, told AFP that Embalo masterminded the coup the outgoing president risked losing the vote.
The country's electoral commission said on Tuesday that it was unable to publish the results of the November 23 presidential and parliamentary elections as its offices had been raided by masked men who destroyed its records on the day of the coup.
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