Lugo has the authority to make the changes "and there is no reason they should be the subject of speculation," the statement said.
The president has now made changes to the senior military leadership on four occasions since he took office 15 months ago, ending 61 consecutive years of rule by the Colorado Party.
'Lack of respect'
In an interview with Al Jazeera's Teresa Bo, Lugo said that while a coup was highly unlikely, "there are a few people that continue to have a relationship with politicians nostalgic of the past that could adventure into something like that, even if I think it impossible."
"More than that, the change in the military responds [is to give] an opportunity to the exceptional young officers that should also have a chance [to be senior officers].
"We don't want to interfere in their chances to participate in the changes in the country. Those are the essential motivations behind the changes that took place in the military structure here in Paraguay."
Benitez, who was set to retire in December, on Thursday defended the sacked officers of the army, navy and air force, and denied there was a plot against Lugo.
Bernardino Soto Estigarribia, a former armed forces commander, told ABC the fired officers had been "humiliated" and tarred with the stigma of being "coup plotters".
The move "shows a lack of respect towards the... members of the armed forces," Soto said.
Lugo is facing rising opposition in congress, with politicians critical of his record hoping to pull together a two-thirds majority to constitutionally remove him from office.
The president's opponents claim that he has failed to crack down on crime and that his administration is corrupt.
Lugo has lost support in congress and among the electorate since three women claimed earlier this year that he fathered their children while he was a priest. In May, he admitted responsibility for one of the children.
Paraguay, surrounded by Brazil, Argentina and Bolivia, has a population of three million and is one of the poorest nations in South America.
Democracy was restored in 1989 at the end of the 35-year dictatorship of General Alfredo Stroessner.
There was an attempted coup in 1996, and the country's vice-president was murdered in 1999.