(Adds details on expected loss, merger throughout)

NEW YORK, April 11 (Reuters) - Bear Stearns Cos BSC.N, the investment bank rescued by JPMorgan Chase & Co (JPM.N: Quote, Profile, Research), on Friday said it will probably incur $288 million of losses in the second quarter stemming from a municipal bond program and a write-down.

Bear did not indicate how large its total losses in the quarter might be.

In a filing with the U.S. Securities and Exchange Commission, Bear said it recognized $200 million of losses related to some trust certificates under a municipal tender option bond program.

Under the program, Bear created securities trusts that buy municipal bonds financed by the issuance of trust certificates. It said that after March 10, holders of all Class A certificates tendered them to the company, causing the loss.

Separately, Bear said it will probably record an $88 million loss to write down goodwill and intangible assets, based on the proposed merger agreement with JPMorgan.

Bear has yet to report first-quarter results, but on Thursday said it expected them to be "significantly lower" than a year earlier, when profit totaled $553.7 million, or $3.82 per share. It also said it expected to file its quarterly report by April 14.

JPMorgan agreed last month to acquire Bear in an all-stock transaction then valued at $10 per share.

Bear said failure to complete the merger would threaten its survival, and could force it to file for bankruptcy protection and liquidate. It expects the merger to close by June 30.