There was no immediate word from Issa, who is pursuing an ongoing investigation into the Sept. 11, 2012, attack that killed U.S. Ambassador Chris Stevens and three other Americans.
The department asked Issa to withdraw the May 29 subpoena, which it said "was issued despite the department having expressed a desire to accommodate your committee's interests and, like the first (subpoena), it arrived while the secretary was traveling overseas representing the United States on urgent national security issues and without confirming the secretary's availability on that date."
The Benghazi attack has become a conservative rallying cry, with Republicans accusing the Obama administration of intentionally misleading the public about the nature of the attack and stonewalling congressional investigators.
In the 20 months since the attack, multiple independent, bipartisan and GOP-led probes have faulted the State Department for inadequate security in Benghazi, leading to four demotions. No attacker has been arrested.
The House voted largely along party lines earlier this month to establish a select, 12 member committee to conduct what will be the eighth investigation into the attack. Seven Republicans, led by Rep. Trey Gowdy of South Carolina, will serve on the panel. Minority Leader Nancy Pelosi, D-Calif., announced this week that Democrats would participate, appointing five members to serve.
The special investigation means there will be high-profile hearings in the months leading up to the elections, with Republicans likely to target current and former administration officials. Almost certain to be called to testify is former Secretary of State Hillary Rodham Clinton.
Issa wants testimony from Kerry, who was a U.S. senator from Massachusetts when the attack occurred, about the Obama administration's cooperation with the congressional panel in providing emails and other documents.