Under EU rules that came into effect in April, border agents must check the documents of all travellers entering the 26-nation free travel area known as the Schengen zone, including European Union nationals, against databases as the block tries to prevent "foreign fighters" returning from Iraq and Syria.
Previously agents only checked the expiration date of the travel documents of European Union nationals and if the photo matched the traveller, which took less time.
Since the rules came into effect, Barcelona airport has seen line ups of up to three hours for travellers because "the number of police officers is not enough," said the representative of Spain's central government in the northeastern region of Catalonia, Enric Millo.
The central government will deploy an extra 50 police officers to the airport, Spain's second busiest, and provide it with another 40 document scanners to resolve the problem, he told radio Rac1.
"The new equipment will arrive in June and its effects will be noticed. We expect the airport will be functioning normally by the start of summer," said Millo.
Catalonia's regional government, which is pushing for the wealthy region to break away from Spain and form its own country, accuses the central government of "sabotaging" the growth of Barcelona airport to ensure it does not surpass Madrid airport in passenger numbers.
"For them, Barcelona airport is a subsidiary airport. I am convinced that this situation would be unthinkable in Madrid," said the minister in charge of infrastructure in the Catalan government, Josep Rull.
Spain's central government argues that the new rules, designed to tackle "foreign fighters" returning from Iraq and Syria, has affected all Spanish airports.
Barcelona airport was especially affected because it has experienced strong passenger growth recently, it added.
Barcelona airport handled 44.1 million passengers last year, an 11.2 percent increase over the previous year, according to Spanish airport operator Aena.
The Schengen zone includes 22 EU countries, plus Switzerland, Iceland, Norway and Liechtenstein.