In a statement, EU foreign policy chief Josep Borrell said there no plans were in place for evacuating Europeans from the country.
A military coup took place after the state election body announced President Ali Bongo had won a third term.
"Naturally, military coups are not the solution but we must not forget that in Gabon there had been elections full of irregularities," Mr Borrell told reporters in Spain ahead of a meeting of EU foreign ministers to discuss the coup in Niger on July 26.
The opposition Alternance 2023 alliance has called for the rest of the votes to be counted in Gabon, urging military leaders to admit their candidate has won.
The alliance also said it was inviting defence and security forces "to the discussion so as to work out the situation within a patriotic and responsible framework and find, among Gabonese, the best solution".
France, where Mr Bongo's loss of power would mark a further blow to Paris's influence in Africa, has condemned the coup and renewed calls "to see the results of the election respected, once they are known".
Mr Bongo has since been placed under house arrest and his cousin Gen Brice Nguema has been appointed transitional head. He will be sworn in on Monday, said Ulrich Manfoumbi Manfoumbi, spokesman for the Committee for the Transition and Restoration of Institutions on Thursday.
Members of the international community have demanded guarantees for Mr Bongo's safety.
Mr Bongo was elected in 2009 after the death of his father, who reputedly amassed a fortune from Gabon's oil wealth.
In 2016 he was re-elected – again in fiercely disputed conditions – before suffering a stroke in 2018 that weakened his grip on power.
Mr Nguema "would like to reassure all donors, development partners, as well as state creditors, that all provisions will be taken to guarantee respect for our country's commitments both externally and internally," Mr Manfoumbi said.
People cheered after the toppling of 55 years of Bongo family rule. However, the army kept a 6pm to 6am curfew "to maintain calm and serenity" and Gabon's borders remained closed.
Five other countries in Africa – Mali, Guinea, Sudan, Burkina Faso and Niger – have undergone coups in the past three years, their new rulers each having resisted demands for a short timetable for returning to barracks.