The government source declined to give any details of the move, citing security concerns.
But Spanish media, including daily El País and National Radio, reported that Madrid would bring close to 250 Afghan citizens, who had already crossed into Pakistan and would be flown out on military transport planes.
The first flight was expected to arrive on Monday evening.
Spain’s evacuations have been weeks in the making, with Foreign Minister Jose Manuel Albares visiting Pakistan and Qatar in early September to lay the groundwork.
Madrid evacuated over 2,000 people, most of them Afghans who had worked for Spain and their families, during the western withdrawal as the Taliban seized power in Kabul in August.
But the flights had to stop once the final American troops that had been protecting the Afghan capital’s airport left.
Prime Minister Pedro Sánchez said in August that Spain would not “lose interest in the Afghans who had remained” in their country but wanted to leave.
The European Union’s top diplomat, Josep Borrell, on Friday urged the bloc’s member states to host a “minimum” of between 10,000 and 20,000 more Afghan refugees.
“To welcome them, we have to evacuate them, and we’re getting down to it, but it’s not easy,” he said in Madrid.
The EU has said a demand by the UN High Commissioner for Refugees to take in 42,500 Afghan refugees over five years can be achieved — although any decision lies with member states.