Khan is tied with Francois Delamontagne, who is 5 under par through nine holes.
Carlos Rodiles and Sergio Garcia share the clubhouse lead at 4-under-par 66. They are joined there by Darren Fichardt, who has completed 12 holes, and David Dixon, who is through nine holes at Pula Golf Club.
Khan dropped in back-to-back birdies from the par-3 second. He jumped to minus-4 with an eagle at the par-5 sixth and picked up a birdie at the ninth to make the turn at minus-5.
The Englishman birdied the 11th to move to 6 under and one shot clear of the field. However, Khan stumbled to a bogey at the 13th to fall back into a share of the lead.
Delamontagne posted a birdie at the first, then ran off three consecutive birdies from the third to jump to minus-4 through five holes. The Frenchman collected his fifth birdie at the par-4 seventh and parred his final two holes before play was called.
Garcia began his round on the 10th tee and picked up a lone birdie over his first nine holes. On the front side, Garcia birdied one and three before faltering to a bogey at the fourth. The Spaniard collected birdies at six and seven to get to 4 under.
'I feel the Spanish fans deserve to watch me play,' said Garcia. 'It's my first time in Spain this year and I'm really happy that I came. I don't come here thinking this is a done deal. I think the field is better than some might think.'
Rodiles also started on the second nine. He birdied the 11th and 18th to head to the front at minus-2 and continued his steady play with pars on the first four holes. Rodiles picked up another birdie at the fifth and climbed to 4 under with a birdie on the ninth.
Robert Karlsson, Santiago Luna and Tomas Jesus Munoz share seventh place at 3-under-par 67. They are tied there by Alastair Forsyth (15 holes), Peter Fowler (12) and Steven O'Hara (9).