Lahoud, who is a Maronite, has faced increasing pressure to resign over the 14 February assassination, particularly since the arrests in the course of a UN investigation into the crime.
"The information which has come to the UN investigation and which has cast suspicion on certain suspects, including those who were in charge of civilian security, is an embarrassment," said a statement from the bishops, who represent the largest Christian community in Lebanon.
The arrests have "given critics a field day," the bishops said, adding that the presidency "should be surrounded by a halo of respect."
They did not comment on calls for Lahoud to resign but said: "We hope a solution will be found to alleviate all doubts."
Maronites want Hizb Allah to disarm
before participating in government
The former security chiefs face charges including premeditated murder, attempted murder, carrying out acts of terrorism and possession of firearms and explosives. If convicted, they face the death penalty.
Al-Hariri's murder triggered massive opposition protests and heightened international pressure on Syria, which pulled its troops out of the country in April after a three-decade military presence.
Lahoud, who first took office in 1998, has consistently dismissed calls for his resignation.
The chief UN investigator into al-Hariri's killing, Detlev Mehlis, has insisted that Lahoud was not a suspect in the case.
The Maronite bishops, who are known for their anti-Syrian positions, have said in a statement that Syrian intelligence operatives are still active in Lebanon.
The statement said the main source of concern is the planting of explosive devices, assassinations and undermining security, particularly in Christian areas.
The bishops also called for resolving the issue of disarming Hizb Allah through "genuine and frank domestic dialogue."