The Congress of Guatemala has voted against lifting President Jimmy Morales' immunity from prosecution, hours after a congressional commission recommended the protection be withdrawn to open the way for a possible trial on campaign finance accusations.

Congress voted overwhelmingly on Monday not to lift the leader's immunity, but since the measure failed to meet a threshold of 105 votes needed to settle the matter for good, it now effectively goes into a dormant state and can be reconsidered in another session of Congress.

Earlier Monday, Julio Ixcamey, head of a five-member commission charged with examining the case, said it had found evidence of unregistered money in campaign funds.

But he also said Morales "did not have a direct participation in registering funds and contributions".

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Last week, the country's Supreme Court said that there appeared to be "sufficient evidence to allow the transfer of the case to Congress". This gave way for legislators to vote on the issue.

Prosecutors allege that about $825,000 in financing for Morales' campaign was hidden and that other expenditures had no explainable source of funding. The president has denied any wrongdoing.

In August, chief prosecutor Thelma Adana and Ivan Velasquez, the head of a UN anti-corruption commission (CICIG) operating in Guatemala, announced they were seeking to have Morales' immunity stripped.

Two days later the president ordered Velasquez's immediate expulsion from the country, but that was swiftly overturned by the Constitutional Court.

Morales won the presidency in 2015, running on a platform of honest governance after his predecessor Otto Perez Molina was forced to resign and was imprisoned in a multi-million dollar corruption case stemming from a CICIG investigation.