Adm. Michael S. Rogers is the head of the National Security Agency and U.S. Cyber Command. (Gary Cameron/Reuters)

The Pentagon and intelligence community are expected to recommend soon to President Obama that he break up the joint leadership of the National Security Agency and U.S. Cyber Command to create two distinct forces­ for electronic espionage and cyberwarfare.

The potential move is driven by a sense that the two missions are fundamentally different, that the nation’s cyberspies and military hackers should not be competing to use the same networks, and that the job of leading both organizations is too big for one person.

Obama was on the verge of ending the “dual-hat” leadership in late 2013 but was persuaded to hold off when senior officials, including then-NSA Director Keith B. Alexander, argued against it on the grounds that the two organizations needed one leader to ensure that the NSA did not withhold resources from Cyber­Com.

Three years later, Defense Secretary Ashton B. Carter and Director of National Intelligence James R. Clapper Jr. are pressing for the split, with Carter seeking to build Cyber Command into a full-fledged fighting force that has its own network accesses to conduct attacks. Clapper, officials said, supports the idea in part to reduce tension over which force gets to use the networks — the spies or the war­fighters.

And with the White House apparently eager to get it done before Obama’s term ends, some officials said that the decision appears all but certain.

Carter and Clapper also favor having a civilian in charge of the NSA, as at the CIA. That would be a break from tradition. Since its inception in 1952, the NSA has been led by a military officer.

The proposed decision reflects a growing debate over how to organize military cyber­operations as they mature and diverge from the intelligence realm that birthed them.

Adm. Michael S. Rogers, the head of the NSA and CyberCom, told an audience at the Intelligence & National Security Summit last week that “I believe in the long run the right thing is to keep these two [organizations] aligned but to separate them.”

But on Tuesday, Rogers clarified his remarks to suggest now is not the time.

At a hearing of the Senate Armed Services Committee, Chairman John McCain (R-Ariz) noted that Rogers earlier this year supported retaining the “dual-hat” relationship. “Is it still your professional advice” that such an arrangement is in CyberCom’s best interests? McCain asked. “Yes,” Rogers replied.

McCain also issued a warning to the administration. If it separated the two organizations, McCain said he would seek to block any nominee put forward to head the NSA if that person is not also picked to lead Cyber Command.

Cyber Command, established in 2009 inside the NSA headquarters at Fort Meade, Md., has long depended on the spy agency’s capabilities. NSA and Cyber Command personnel sit side by side and use the same networks that were built by the agency.

But after revelations of NSA surveillance programs by former contractor Edward Snowden, a presidential commission recommended that the NSA and Cyber Command be separated, arguing that the intelligence-gathering and combat functions have distinct targets and purposes. The spies want to steal information without getting caught. The fighters want to disrupt systems and don’t mind if the enemy knows who did it.

Carter has brought Cyber Command into the fight against the Islamic State and wants it to act openly, like other military commands, rather than as the annex of a highly secretive spy agency. He also wants Cyber Command to control the resources it needs.

“Whether or not it’s true, the perception with Secretary Carter and [top aides] has become that the intelligence agency has been winning out at the expense of [cyber] war efforts,” said one senior military official, who like other officials interviewed for this article spoke on condition of anonymity because he was not authorized to discuss the issue publicly.

The Office of the Director of National Intelligence and the Pentagon declined to comment.

“We are constantly reviewing if we have the appropriate organizational structures in place to counter evolving threats, in cyberspace or elsewhere,” one senior administration official said. “While we have no changes­ to this structure to announce, the relationship between NSA and Cyber Command is critical to safeguarding our nation’s security.”

Some former officials believe that Cyber Command can never be fully independent of the NSA and that it makes no sense to cleave one from the other.

“When you have two organizations whose missions overlap or touch, unless you have some way to control both of them, then they will instantly go to war with each other,” one former senior intelligence official said.

“Cyber Command’s mission, their primary focus, is to degrade or destroy,” the former official said. “NSA’s is exploit [to gather intelligence] only. So without having one person as the leader for both, the bureaucratic walls will go up and you’ll find NSA not cooperating with Cyber Command to give them the information they’ll need to be successful.”

On Capitol Hill, the Senate Intelligence Committee has put language in its 2017 intelligence authorization bill that bars the NSA director from serving at the same time as the Cyber Command head. The Senate Armed Services Committee, however, is reluctant to see a split until the defense secretary and chairman of the Joint Chiefs of Staff certify to Congress that such an arrangement will not “pose risks” to the military effectiveness of Cyber Command.

There is a uniform agreement, however, that if joint leadership is ended the two organizations must still work closely. They would need to ensure that their operations don’t interfere with each other’s and that the NSA must continue to supply CyberCom with intelligence.

Military officials said that Cyber Command could develop its own network nodes or accesses to carry out missions independent of the NSA, although some are skeptical that it can be done without spending substantial sums to duplicate the NSA’s infrastructure.

“The country can’t afford it,” the former intelligence official said. “NSA’s a trillion-dollar investment.”

Others disagreed. “It’s not like you have to rebuild all of NSA in order for Cyber Command to be independent,” a second administration official said.

If the separation goes forward, a key challenge will be funding for Cyber Command to develop the capabilities it needs. The command is still building up its force structure, aiming for 6,200 personnel by October 2018.

Missy Ryan contributed to this report.