Section 538 Improvement Act of 2009 - Amends the Omnibus Appropriations Act, 2009 regarding the Rural Housing Service-Rural Housing Insurance Fund Program Account.
Repeals the declaration that, for applications received under the 2009 notice of funding availability, section 538 multi-family housing guaranteed loans funded under such Act shall not be subject to a guarantee fee and the interest on such loans may not be subsidized.
Authorizes the Secretary of Housing and Urban Development (HUD) to: (1) reduce the funding under such Act for section 538 multi-family housing guaranteed loans by up to $29.09 million; and (2) use such amounts as equivalent funds to subsidize the interest on such guaranteed loans for which applications are received under the 2009 notice of funding availability.