"The website was temporarily redirecting all specific press release pages to the home page," Mr Trump spokesman Steven Cheung said in an email.
Links to Mr Trump's policy proposals, including the Muslim ban, are now working again.
The links, which had redirected readers to a campaign fundraising page, appeared to have been removed around election day, when Mr Trump won a historic upset against Democratic rival Hillary Clinton, according to a website that records historic snapshots of web pages.
In an appearance on CNBC, Saudi Prince Alwaleed bin Talal praised Mr Trump for removing the Muslim ban proposal from his website and also said Mr Trump had deleted statements offensive to Muslims from his Twitter account.
The prince could not be reached for comment after the links were restored.
Several tweets attacking Muslims that Mr Trump sent while campaigning for president remained in his feed on Thursday, including this March 22 tweet:
✔@realDonaldTrump
Incompetent Hillary, despite the horrible attack in Brussels today, wants borders to be weak and open-and let the Muslims flow in. No way! 1:29 PM - 23 Mar 2016
After initially praising the removal of the Muslim ban proposal at a news conference with other civil rights leaders, Samer Khalaf, president of the American-Arab Anti-Discrimination Committee, said in a follow-up interview the group was hoping to see better behaviour from Mr Trump.
"False hope just came over us," Mr Khalaf said, but "we didn't really think it was monumental that they took down the language". Analysis
Mr Khalaf said Mr Trump's policies were more important than any statements.
"He's elected, he said some horrible things, now we have to see what his policies are," he said.
"If they're good policies we're going to commend him for it. If they're horrible policies we're going to challenge him on it."
Despite the temporary glitch, most of Mr Trump's core policy positions had remained on his website, including his central immigration promise to build an "impenetrable physical wall" on the border with Mexico and make Mexico pay for its construction.
It was not the first time the Trump campaign blamed technical difficulties for changes to its website.
The campaign this year also replaced the part of the site describing Mr Trump's healthcare policy with a different version. When contacted about it by Reuters in September, the campaign put the original page back up.
PHOTO: Donald Trump claimed an upset result in the US election (AP/Evan Vucci
Donald J. Trump
