While the German, who reached last year's final, did eventually suppress the Belgian's unorthodox game to win 7-5 7-5, she again showed signs of the vulnerability that has dogged her in 2017.
Having claimed the Australian and U.S. Open crowns last year, Kerber has not won a single title this season and suffered an ignominious first-round exit from the French Open in May.
For large parts of Thursday's encounter on Court One, she struggled against Flipkens, who tried everything in her power to upset the world number one.
News that makes sense
Your trusted source for staying up-to-date with the world around you. Get free daily news updates and analysis, straight to your inbox.
Once again Kerber's serve and groundstrokes seemed to lack the potency they possessed last year, which appeared to encourage Flipkens to pile on the pressure in the evening gloom.
At times in the first set Kerber found Flipkens' game unfathomable as the Belgian tried her luck with a number of perfectly weighted drop shots and low slices, while frequently charging the net in an effort to upset the German baseliner.
The pair exchanged four successive breaks of serve before Kerber regained her composure to hold and then broke Flipkens for the third straight time to reassert her authority before taking the first set.
It was another even battle in the second as the players exchanged breaks before Kerber struck decisively in the 11th game and then served out to win in one hour 44 minutes.
"I think it was not an easy match ... Kirsten is always tough to play because she plays good on grass with the slice," Kerber told reporters.
"I couldn't find my rhythm in the first few games, but then I was trying to move good and playing the ball back. It was for sure maybe not the best tennis that I played, but I was trying to fight again for every point, and I think that was the key at the end."
(Reporting by Toby Davis; Editing by Ken Ferris, Larry King)
