The 30-year-old Englishman made the turn at 5 under at Barseback Golf Club, then had to wait for an hour before continuing because of a thunderstorm warning. Slattery finished with seven birdies, playing in the first group early in the morning.
His only mishap came on the 12th, the shortest par-5 hole on the course where he made a bogey after hitting a tree.
Slattery, ranked 504th in the world, led Ricardo Gonzalez of Argentina by one shot. Klas Eriksson of Sweden, Spaniards Pablo Larrazabal and Pablo Martin Benavides, and Tano Goya of Argentina were another shot back in third.
Henrik Stenson of Sweden, ranked seventh in the world and a member of Barseback, shot 73.