Continental operates a large hub out of Newark and has about 3,000 daily flights system-wide. It was working to get customers on alternate flights.
Airline spokeswoman Megan McCarthy said that the cancellations were "due to lack of crew availability" but declined to elaborate. Air Line Pilots Association spokeswoman Amy Flanagan declined to comment.
United Airlines bought Continental last year and has been trying to combine them into a single airline. The process has been slower than expected, partly because of contentious labor negotiations.
Jeff Smisek, the CEO of United Continental Holdings Inc., said last week that it was unlikely the company could agree to labor contracts with all its unions this year.
The company said it has more pilots this summer than last summer. Company spokeswoman Julie King said the Air Line Pilots Association, which represents pilots at both airlines, "participates in our monthly review to set staffing levels."