In a 32-page decision penned by Justice Edilberto Sandoval, the anti-graft courts second division also acquitted former city engineer Vivencio Patagoc and planning engineer Edgardo Tarife.
However, the case against the fourth respondent, project engineer Henry Lood, was "archived" because he is nowhere to be found. The case will be revived upon his arrest, the court said.
Sandoval and fellow Justices Raoul Victorino and Godofredo Legaspi said Agan is presumed to have performed his duties regularly because he himself admitted having issued the travel orders.
"It is glaringly evident that the authorities to travel were approved legitimately and properly. The record is replete of concrete proofs linking to the compliance with or accomplishment of the purpose stated in the questioned authorities to travel," the court said.
The Sandiganbayan noted that the government incurred no losses even if the three engineers used public funds in going to Manila in April 1994 because the purpose of their travel to attend their arraignment for cases in the Sandiganbayan was justified.
The prosecution, the anti-graft court said, failed to show that Agan abused his powers in issuing the travel orders on April 20 and Aug. 17, 1993 and Feb. 14, 1994.
"We are persuaded from a study of the cases that the evidence adduced was not adequate to show that Agan was actuated by dishonest purpose or ill-will partaking of a fraud or some furtive design or ulterior purpose to do wrong and cause damage," the court said.