A US government lawyer told a Virginia court 100,000 visas had been revoked.
But the State Department said it was 60,000, once diplomatic and expired visas were taken out of the equation.
The directive - which bans people from seven mainly Muslim Middle Eastern and African countries from entering the US - has led to widespread protests.
Courts in at least five US states - Virginia, New York, Massachusetts, Michigan and Washington - are hearing cases challenging the White House executive order.
Trump border policy: Who's affected?
The 100,000 figure emerged on Friday in a hearing at Alexandria, Virginia, for two Yemeni brothers deported after their arrival at Dulles International Airport last Saturday.
The number was cited by US Justice Department lawyer Erez Reuveni, who added that no Green Card holders had been denied US entry.
Simon Sandoval-Moshenberg, one of the plaintiffs' lawyers, said after the hearing: "There is no legal justification to cancel all these visas."
The latest reaction to the executive order included:
The White House said on Monday that only 109 people were "slowed down" in their travel out of 325,000 people who had flown into the US since the order was given.
State Department spokesman Will Cocks said they were aware individuals who had their visas revoked would be "temporarily inconvenienced".
But he said national security was the administration's top priority when approving visas.
The State Department said it issued over 11 million immigrant and non-immigrant visas in 2015.
Several judges have granted temporary restraining orders barring US authorities from enforcing portions of Mr Trump's ban.
President Donald Trump's immigration executive order has led to the cancellation of tens of thousands of US visas, officials say.