In this photograph taken on April 20, 2013, former Pakistani president Pervez Musharraf is escorted by soldiers on his arrival at an anti-terrorism court in Islamabad. (AAMIR QURESHI/AFP/Getty Images)

A Pakistani court on Tuesday indicted former president and army chief Pervez Musharraf on murder charges in connection with the 2007 assassination of former Pakistani prime minister Benazir Bhutto, dealing a further blow to a once-powerful figure who returned to the country this year to make a political comeback.

The decision by a court in Rawalpindi marks the first time that Musharraf, or any former army chief in Pakistan, has been charged with a crime.

Musharraf, who took power in a 1999 coup and stepped down from office in disgrace nearly a decade later, faces a host of legal problems that in many ways have broken taboos on the inviolability of the once-sacrosanct military in Pakistani society. He is under house arrest in connection with one of the cases against him.

The retired general was charged with murder, conspiracy to commit murder and facilitation of murder, said prosecutor Chaudhry Muhammed Azhar. He did not specify what Musharraf was accused of doing, but prosecutors have previously accused him of failing to provide Bhutto with adequate protection.

Musharraf had earlier been arrested on accusations that he had played a role in the assassination, but the legal proceedings Tuesday mark the first time that the government has formally charged him with a specific crime in Bhutto’s assassination.

The former army commando appeared in person during the brief morning hearing Tuesday and pleaded not guilty, said Afshan Adil, a member of Musharraf’s legal team.

“These are all fabricated cases. There is nothing solid in all these cases,” she said.

Bhutto was killed in 2007 during a gun and bomb attack at a rally in Rawalpindi, the sister city of the Pakistani capital, Islamabad. Bhutto, the daughter of former prime minister Zulfiqar Ali Bhutto, who was executed in 1979 after being deposed in a coup, was respected in Pakistan for her political commitment — she was jailed multiple times — and her condemnation of militancy and support for Pakistan’s poor. But her terms were marred by accusations of widespread corruption against her and her husband.

She returned to Pakistan under a deal with Musharraf allowing her to take part in upcoming elections, and his supporters point to the deal as proof that he had no objections to her return.

Her assassination set off a wave of protests across the country and helped propel her Pakistan People’s Party to office and her husband, Asif Ali Zardari, to the presidency.

A 2010 U.N. report on the circumstances surrounding her death was highly critical of steps taken by Pakistani investigators, including the hosing down of the crime scene, the failure to perform an autopsy and their media conference the day after in which they blamed a Taliban commander.

The report also said that Musharraf failed to make serious efforts to ensure Bhutto’s safety. His supporters have dismissed the report’s findings.

The judge set Tuesday as the next court date for lawyers to present evidence.

Musharraf returned to Pakistan in March after nearly four years outside the country and vowed to take part in the May elections. But he has little popular support in Pakistan and since his return has faced a slew of legal problems related to his rule.

Musharraf has said repeatedly that he returned to lead his supporters in the election and that he would clear his name of all charges. But many questioned his decision to come back, considering the legal problems he would face and his almost-nonexistent popularity.

His return and legal troubles have put the military and newly elected Prime Minister Nawaz Sharif in a delicate position. Pakistan has undergone three coups since the country’s inception in 1947, and the military is considered the country’s most powerful institution.

The military’s top leaders are not thought to have supported Musharraf’s return from exile, but they also would probably not want to see one of their own put behind bars or treated unfairly.

— Associated Press