Hundreds of companies that owed the city $6.4 million in unpaid parking tickets for more than 30 days still managed to get special discounts available only to fleets that paid their summonses on time, Comptroller John Liu reported yesterday.

Liu’s auditors found that 1,517 companies enrolled in two discount ticket programs owed $9.3 million in April 2012, with two-thirds outstanding more than 30 days.

In return for prompt payments within 15 days, the companies were entitled to fine reductions of 20 or 30 percent.

“It’s bad enough that people feel like they’re getting blitzed with parking tickets,” said Liu. “It’s absolutely galling to now find the city lets big companies off the hook on million in parking tickets.”

The Department of Finance, which oversees ticket collections, dismissed Liu’s audit as misleading and out-of-date.

Officials said large sums are outstanding at any given point in time — but are eventually collected.

“The fact is Finance has collected 99 percent of the revenue associated with fines issued to companies enrolled in the programs over the past two years,” said Finance spokesman Owen Stone.

Finance officials also said it has been working for months on a revamped computer system that will go up “within the next few weeks” creating an on-line portal for all new tickets.

“This has been going on for eight years,” countered a Liu aide, adding that not a single company has ever been kicked out of the discount program for late or non-payments.