Asuncion, Paraguay (CNN) -- Paraguay installed new top military commanders, but President Fernando Lugo, who had ordered the change in leadership, was not present for the ceremony.
Lugo's absence Thursday morning attracted attention given his administration's silence on the sudden change in the leadership of the country's army, air force and navy.
The president's decision to replace the top brass came a day after he publicly dismissed rumors about a military coup.
Brig. Gen. Bartolome Ramon Pineda Ortiz was named as the new army commander. Brig. Gen. Hugo Gilberto Aranda Chamorro and Rear Adm. Egberto Emerito Orie Benegas took over the top posts at the air force and navy, respectively.
The announcement came from the armed forces, not the president's office.
Cibar Benitez, commander of the armed forces, was the only top leader to retain his post.
Other changes would be forthcoming in the lower ranks, said Benitez at the swearing-in ceremony, but he denied there was any truth to talk of a coup.
Paraguay's history is filled with unstable transitions of power since it emerged from dictatorship in 1989. Although there hasn't been a coup since that year, there were attempted coups in 1996 and 2000, and President Raul Cubas resigned amid controversy in 1999.
The military shakeup is the third since Lugo took office. The former Catholic bishop was elected to a five-year term last year. His victory brought an end to six decades of one-party rule in Paraguay, but the honeymoon did not last long.
In April, Lugo admitted that he fathered a child while he was still a priest and that he may have fathered more. The revelation, which came as a shock to most, hurt his political image. Calls for his resignation began, and have continued as Lugo has struggled to push reforms through a majority-opposition legislature.
Journalist Sanie Lopez Garelli contributed to this report.