Bolivia's justice ministry on Monday accused former president Evo Morales of a second alleged sexual relationship with a minor, authorities said.

The 60-year-old, who led the South American nation from 2006-19, allegedly fathered a child with the girl when she was just 16.

The latest accusation comes after the justice ministry filed a complaint with the public prosecutor last week against Morales for "statutory rape and human trafficking."

The ministry revealed on Monday "a possible new case of rape" following an anonymous complaint, Deputy Minister Guido Melgar said.

It has filed a report with the La Paz ombudsman for children and adolescents, which can investigate the allegations.

Authorities established that the girl "had a sentimental relationship with Juan Evo Morales Ayma and fell pregnant when she was 15 years and five months old," Melgar said.

He added that she gave birth to a girl in February 2016 when she was 16.

"The minor exists. The mother exists and the minor's registered father is Juan Evo Morales Ayma," said Melgar.

The birth document was passed to the ombudsman to investigate and then decide whether to file a criminal complaint with the public prosecutor.

Rape is punishable under Bolivian law by between two and six years in prison.

Last week's complaint came after Bolivian newspapers published photographs showing Morales with a young woman, identified by the initials N.M.

Now 19, she was reported to have been a minor when their relationship began.

Morales's Movement for Socialism (MAS) party claims the accusations are politically motivated and blames the conservative interim government.

Bolivia is gearing up for presidential elections on October 18 and although Morales is barred from standing, even as a legislator, his party's candidate Luis Arce has consistently led polls since he was nominated in January.

MAS say the government is using the accusations to try to influence the election.

Morales has lived in exile in Argentina since fleeing weeks of post-election violence after his controversial re-election last October.

His country's first indigenous president, he had stood for an unconstitutional fourth term but an Organization of American States audit found evidence of electoral fraud.