The 41 year old Northern Irishman, on course not only for a first win in two years but also a place in next week's Open Championship, birdied the 425 yard first for the second day running.
Clarke was up to 11 under par as a result in what has so far proved to be a dream week. On Monday and Tuesday he won the star-studded JP McManus Invitational Pro-Am featuring Tiger Woods at Adare Manor in west Ireland.
Italian Edoardo Molinari parred the opener to remain in second place, while Welshman Bradley Dredge was left alone in third at six under when Swede Peter Hedblom bogeyed the second.
Clarke's compatriot Graeme McDowell, playing his first European Tour event since lifting the US Open Championship last month, has warned people not to expect too much this week, but he was up into a tie for 12th on three under after going to the turn in 33.
One better than that after a joint best-of-the-week 65 was England's Ross Fisher and that was a valuable boost to his hopes of a Ryder Cup debut in October.
Fisher, winner of the Volvo World Match Play last October and second in the BMW International Open in Munich two weeks ago, stands 12th in the points race.
Welshman Rhys Davies, three places behind him, threatened to make a big move too when he eagled the third and birdied the next, but bogeys on the seventh and 11th dropped him back to level par.
Earlier, Australian Brett Rumford was disqualified before he teed off again after realising he had signed for a wrong score.
Rumford took a bogey four on the short 17th in his second round, but a three was put on his card by playing partner Sam Little, who was marking it.
Molinari responded to Clarke's opening 15-foot putt with one from over 40 feet on the next and then hit a brilliant fairway wood to six feet at the long third and eagled.
Clarke had his second birdie there, but his lead was down to two.
Hedblom also birdied the hole, but he and Dredge were now six behind Clarke in joint third spot.
Clarke's advantage was down to one when he bogeyed the short fifth - only his second dropped shot at the week - and when Molinari made a ten footer on the long next they were level at 11 under.
By then, though, Clarke had hit his approach to three feet and with that he moved one ahead again at 12 under.