Dan Eliasson had told Euronews he considered his Canary Islands trip to be "of personal importance" despite government advice against travelling abroad.
A senior Swedish official resigned after he was widely criticised for holidaying in the Canary Islands over Christmas during the COVID-19 pandemic.
Dan Eliasson, head of the Swedish Civil Protection Agency (MSB) since March 2018, had travelled to the Spanish islands to visit his daughter despite government recommendations against foreign visits.
In a statement to Euronews, the agency had initially said their director-general considered the trip on 30 December to be "of personal importance."
Although he did not break the law, Eliasson's trip sparked anger and indignation in Sweden.
Earlier that month, his own agency had sent out text messages to Swedish citizens urging them not to travel abroad.
"The important thing is not me as a person," Eliasson said in a statement on Wednesday.
"The important thing is how we as a society handle the pandemic and that all focus is on the incredibly important task.
"The reason for my position is that MSB as an authority should have the best possible conditions to carry out its important assignment."
His resignation comes after a meeting with Home Affairs Minister Mikael Damberg, as the Scandinavian country battles a recent spike in coronavirus cases.
In a further statement, the MSB said that the head of their authority had resigned after seeing the reactions at the meeting.
Unlike other European nations, Sweden has never introduced a full lockdown or closed businesses during the pandemic, relying instead on citizens' sense of civic duty to control infections.
Other senior figures in the country's government have also faced pressure for their actions during the health crisis, including Minister for Finance Magdalena Andersson, who was photographed renting skis at a popular Swedish resort just before Christmas.