As Guatemalan President-elect Jimmy Morales prepares to take office Thursday, members of his own political party currently face legal charges for alleged human rights violations, which took place during the 1960-1996 civil war.

Last Wednesday, Attorney General Thelma Aldana announced a legal investigation into Edgar Justino Ovalle Maldonado, the co-founder of Morales’ Convergence Party and one of the incoming president’s top advisers. The party is also backed by a number of other former military officials who fought in the country’s war that the U.N. said amounted to genocide against the Guatemala’s Indigenous population

Ovalle is being prosecuted for his role in leading military operations in the Quiche region where 77 massacres took place during the country’s most horrific period of genocide during the early 1980s.

Attorney General Aldana has asked the Supreme Court to lift Ovalle’s immunity which he enjoys as a newly elected member of Congress so that the former military commander and current member of Congress can be prosecuted for overseeing grave human rights violations during the civil war.

Aldana also announced the arrest of 14 former military officials involved in hundreds of forced disappearances and crimes against humanity in one of the Central American country's bloodiest eras in history.

The detained military officials are linked to the forced disappearance of at least 558 people, whose remains were recovered in a clandestine mass grave in Guatemala’s Coban area, home to a former military base.

...22 of the Coban skeletons were infants. The Guatemalan perpetrators of the crime are being arrested. The North Americans remain at large.

— Allan Nairn (@AllanNairn14) January 10, 2016

The recent arrests and high-level investigations take place days ahead of President Morales’ inaugural ceremony on Jan. 14, shifting the focus on the links between the FCN and former military officials.

RELATED: Guatemala Arrests 14 Ex-Military Officials Linked to Genocide

The military ties to Morales’ Convergence party remain a concern to both citizens and analysts who worry that efforts to prosecute former military officials accused of human rights violations committed during the country’s civil war may be impeded or halted altogether.

The Morales administration’s links to questionable Guatemalan military figures is further called into question when examining members of his inner circle.

Colonel Erick Melgar Padilla, a former high-ranking military officer is rumored to be the country’s next Minister of Defense. Meanwhile, his brother, former Colonel Armando Melgar Padilla was head of Morales’ private security team and is also expected to hold influence in the new Morales government.

Investigative journalist Luis Solano has repeatedly linked the Melgar brothers to the 2007 high-profile killings of three Salvadoran members of the Central American Parliament. Solano alleges that the Salvadoran lawmakers were killed and subsequently burnt on two separate property holdings owned by the Melgar Padilla family. According to the journalist, the Salvadorans were initially tortured in a chapel on the Parga estate, which since 2005 had allegedly been used as a site by the Guatemalan National Police to torture gang members and drug traffickers.

OPINION: Rios Montt Case Symbolic of Impunity Guatemalans Must Overcome

Impunity for serious modern day and civil war era crimes has plagued Guatemala for decades, and not only have the perpetrators evaded justice, but many have continued to run the country. Whether the self-described political outsider Morales decides to try dismantle this institutionalized impunity, even as his political party has ties to it, remains to be seen.