There are "lessons to learn" after the decision to remove Spain from the list of countries exempt from quarantine, Humza Yousaf has said.
The Justice Secretary said the change was made after "deeply alarming" data emerged showing cases almost doubling in Spain.
He said it is "inevitable" that countries that are currently on the exempt list for quarantine will be removed as spikes in coronavirus cases emerge.
The decision to remove Spain from the list was made on a "four nations" basis on Saturday, with the UK Government and all devolved administrations ordering returning travellers to self-isolate for 14 days.
Speaking on the BBC's Good Morning Scotland radio programme, Mr Yousaf acknowledged how "frustrating and disappointing" the situation was for many tourists, but said travel during the pandemic would always have an element of risk.
He said: "The reason is very much based on the public health data we received on Saturday from the UK Government that showed a deeply alarming trend in Spain.
"In the space of a week, from the 17th of July to the 24th of July we saw cases in Spain almost double from 5,700 to 11,000."
Asked if it was a mistake to take Spain off the quarantine list a few days ago, he said: "When we made the decision to remove Spain, the decision was based on the data.
"So the prevalence, which is the percentage of the population per 100,000 that is infectious, that has dramatically reduced, in fact it was lower than what Scotland's was ...
"Clearly on reflection, perhaps there are some lessons for us to learn, I'm never against us doing that.
"I think that's important for us to do, particularly because without a global vaccine being available there are going to be times when countries are going to be taken off the exempt list, put back on the list, depending on the data that we receive."
He said travel during a global pandemic would always carry "some element of risk" as the situation could change rapidly.
Mr Yousaf said: "Of course I understand why people will be disappointed, I understand why people would be frankly quite angry.
"But I hope people understand that the only reason we choose to make decisions is based on the public health data we receive and is in the best interests of keeping people safe here in Scotland."
The Economy Secretary was in touch with travel companies to discuss support, he said.