The Duke and Duchess of Sussex have been forced to apply for retrospective planning permission for landscaping at the cottage, because it is different to the design already approved by the council.
While retrospective planning applications can be submitted for work already carried out, permission won't automatically be granted.
According to the Daily Mail, if the application is refused, the council can issue an enforcement notice which could require the couple to reverse any changes made at the Grade-II listed cottage.
While the exact details that have changed remain unclear, there has been an outcry over the threats to national security if the proposals are made public - something which could happen if the council puts the plans on its website or in its offices.
Ian Ratcliffe, project manager at the Royal Household, said in a letter to the council that details of the couple's plans should be kept secret, said Daily Mail's report.
"National security could be compromised if public access is given to the plans", he said.
He argued that copies should not be sent to statutory consultees, as is typical of these applications.
"For reasons of national security, we would appreciate if this application could be treated as confidential, and not be allowed to enter the public domain."
Newlyweds Meghan and Harry moved into the royal residence in April, before welcoming baby Archie Harrison on May 6.
While initial reports had talked of a yoga studio and other lavish additions to the property, sources close to the couple told The Daily Mail that reports of a yoga studio or "floating floors" at Frogmore Cottage were incorrect.
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