Net profit in the three months to June 30 was 7.83 million dinars ($28.7 million), the company said in a statement, down from 18.09 million dinars a year earlier.
Two analysts had forecast in a Reuters survey that Agility's second-quarter earnings would fall to an average of 7.4 million dinars.
Agility blamed the drop in earnings and a 23 percent fall in quarterly revenue to 331 million dinars on lost defense and government business.
The company said it expected solid gains in 2012 as its investments in emerging markets were helping the growth of its core business, and its customer base was expanding while operations were being streamlined.
Fresh initiatives intended to grow revenue and reduce costs should produce solid gains in 2012, Agility said without giving details.
Last month, a U.S. district judge ordered the arraignment of Agility in the latest step of the prosecution of the logistics company over charges that it defrauded the U.S. Army in multibillion-dollar contracts.
The order came on the heels of a decision by a U.S. appeals court that ended about 18 months of legal wrangling over whether prosecutors correctly served the company in its initial indictment in November 2009.
Agility was the largest supplier to the U.S. Army in the Middle East during the war in Iraq after 2001's September 11 attacks, with contracts worth around $8.5 billion.
Agility's shares ended 2 percent lower on Sunday. The results were released after the market closed.
(Reporting by Eman Goma; Writing by Firouz Sedarat; Editing by Mike Nesbit)