Cruise, 50, was spotted carrying Suri into a New York hotel where he is staying, reported TMZ online.
"He has been dying to see her," a source said.
The father-daughter duo's day began when Cruise flew in from Los Angeles after wrapping the shoot for his film "Oblivion".
He picked up Suri from Holmes's apartment. Both Cruise and Holmes did not see each other. He was reportedly only there for about five minutes.
Part of their day together included him taking Suri to her gymnastics class at the Chelsea Piers.
It is reported that the father and daughter will spend several days together while he is in town.
The last time Cruise was publicly seen with his daughter was while he and Holmes were still married and the three were out for dinner in Iceland.
"Katie wants to make sure the visits are in the context of him being a parent figure. He adores Suri, but now he's afraid he won't be able to have a close relationship with her," said a source.
R&B star Rihanna and rapper Drake are leading the MTV Video Music Awards (VMA) nominations with five nods each.