McIlroy's poor start to 2013 continued at Palm Beach Gardens last week as he pulled out midway through the tournament citing wisdom tooth pain.
The Northern Irishman, who recently changed club manufacturer, also missed the cut in Abu Dhabi at the start of the year before a surprise first-round defeat at the WGC Matchplay.
"I talked to him on Monday prior to the tournament and he told me he was struggling," said Nicklaus.
"He said he was driving the ball well but was struggling a little bit with his irons, but he felt confident out there.
"He's probably not playing at his best, and he also has a set of golf clubs he's having trouble getting used to. One plays off against the other. He'll be fine."
McIlroy is due to return to action on March 7 at the WGC Cadillac Championship in Miami, Florida.