Washington (CNN) White House chief of staff John Kelly has been locked in an internal struggle with President Donald Trump's son-in-law and senior adviser Jared Kushner over his access to highly classified information for weeks now, a confrontation that has escalated amid a recent policy overhaul and the resignation of a staff secretary who was accused of spousal abuse.

The dispute has deepened a growing rift between Kelly and Kushner, who initially welcomed the new system of rigor instituted by the chief of staff but has since grown frustrated by what he views as attempts to limit his access to the President.

Kelly distributed a five-page memo Friday announcing that the White House will no longer allow some employees with interim security clearances to access to top secret information if their background investigation has been pending since before last June -- a category Kushner falls into.

Some saw the memo as a direct affront to Kushner, who has had access to highly classified information for over a year but still does not have a permanent security clearance. Kushner is one of the few White House officials who regularly receives the President's Daily Brief, a daily roundup of issues that the intelligence community determines the President needs to be aware of each morning.

"It's not aimed at Jared, but to fix a broken system," a White House official said, acknowledging the tensions that exist between Kelly and Kushner.

But since Trump has the ultimate authority over who he does -- and doesn't -- want in his inner circle, it's far from clear whether Kelly's new policy will be immediately enforced on Kushner, the official said. The new clearance policy could limit Kushner's ability to participate in meetings or handle documents with classified information, a strategy some say is intentional on Kelly's behalf.

Kushner has taken an active role in foreign policy in the Trump administration, and has requested access to more classified information than most other top White House aides, according to a person familiar with the matter.

However, the person downplayed the extent to which his biggest portfolios -- including attempting to broker a peace agreement between the Israelis and Palestinians and working with China on trade issues -- would require access to highly classified information. Instead, the person said, those matters could be walled off without requiring access to other government secrets.

Fallout from Porter scandal

Kelly's new process for granting security clearances comes a little over a week after former staff secretary Rob Porter resigned when abuse allegations against him became public. Kelly has been the subject of criticism in that time over revelations that Porter remained on staff for months in spite of the FBI flagging the allegations of domestic abuse to the White House. In his memo, Kelly acknowledged that that "we should -- and in the future, must -- do better."

One White House official said that, although unspoken, it was clear that other staffers were worried about raising questions about Porter's clearance issues because they were concerned it would resurrect scrutiny surrounding Kushner's own issues.

Though Kushner and Ivanka Trump were once proponents of Kelly, believing he would bring much-needed stability to a chaotic West Wing, neither thought the limitations he would impose would apply to them. They have, in turn, soured on him. The pair has actively discussed possible replacements for Kelly, including Gary Cohn, who is currently Trump's top economic adviser.

Multiple White House officials have said the complications with Kushner's security clearance have only exacerbated his frustration with Kelly, who has privately disregarded Kushner and Ivanka Trump as unserious and meddling. Since becoming chief of staff, Kelly has sought to limit Kushner's portfolio while also dismissing Ivanka Trump's agenda, once referring to her child tax credit as "a pet project."

One White House official speculated that the security clearance restriction could also serve as a way for Kelly to limit Kushner's access to the President, because he would be restricted from attending certain briefings or participating in sensitive conversations.

Though a source familiar with the situation said Kushner has not yet appealed to the President directly about his access to highly classified information, those close to Trump believe he would be inclined to grant his son-in-law access if asked. This source pointed to the fact that Kushner is part of the President's family and has outlasted all of his rivals in Trump's inner circle, including former chief of staff Reince Priebus, former chief strategist Steve Bannon, former campaign manager Corey Lewandowski and former deputy campaign manager David Bossie.

Trump, however, has given Kelly his full support in efforts to reform the White House's system of security clearances, and has told his chief of staff that changes need to be made to bring the system into order, according to a person who has spoken to him about the matter. Kelly has interpreted that as a wide-ranging mandate that would include Kushner, a person familiar with the matter said. The person said Trump and Kelly would likely discuss the matter this week, if they haven't already, before Kelly's self-imposed Friday deadline.

Kelly's job safe -- for now

Despite a swirl of reports last week about Kelly's standing in the West Wing, multiple people who spoke with Trump over the weekend say he does not appear any closer to dismissing his chief of staff. Kelly spent the weekend in Florida with the President at his estate in West Palm Beach. The President also told Kelly privately that he has his support, adding that he "had a hell of a week" and emerged stronger.

Kelly, who has told colleagues he considers himself to be media savvy, has been cautious to appear publicly supportive of Kushner. After questions were raised whether the new clearance policy would affect Kushner, Kelly issued a statement saying he had "full confidence in (Kushner's) ability to continue performing his duties in his foreign policy portfolio including overseeing our Israeli-Palestinian peace effort and serving as an integral part of our relationship with Mexico."

"Everyone in the White House is grateful for these valuable contributions to furthering the President's agenda," Kelly said. "There is no truth to any suggestion otherwise."

Kelly also coached White House press secretary Sarah Sanders on how to answer when asked about Kushner's clearance issues.

"I can tell you that nothing that has taken place will affect the valuable work that Jared is doing. He continues, and will continue, to be a valued member of the team," Sanders said at the briefing Tuesday. "And he'll continue to do the important work that he's been focused on with the last year."