NEW YORK, May 31 (Reuters) - The Colonial Pipeline, the largest pipeline system for refined oil products in the U.S., on Friday informed shippers that it has filed to increase rates for the majority of shipments on its more than 5,000-mile network.

The pipeline operator submitted filings with the Federal Energy Regulatory Commission (FERC) to increase all rates as of July 1, except on those for short-haul fuel deliveries in the northeastern part of the country.

The rate hikes are based on FERC's index-rate formula, used by the regulator to track changes in recoverable pipeline costs and updated annually in May based on market conditions. The index-rate tariff hikes for this year round up to about 1.26%.

The pipeline has also filed to increase market-based rates for Gulf-to-Gulf and Gulf-to-Northeast markets.

Shippers can contest pipeline rates by filing a protest or complaint with FERC in response to the hike. (Reporting by Shariq Khan in New York; Editing by David Gregorio and Paul Simao)