WASHINGTON — The Municipal Securities Rulemaking Board’s net assets fell to $26.39 million for the fiscal year ending Sept. 30, 2009, down $1.65 million from the previous year as new underwriting assessment fees fell dramatically, according to an audited financial statement and annual report expected to be released by the board today.

The MSRB annual report, which for the first time also includes annual financial information, reveals that the board’s financial position was “significantly affected” by the economic crisis and a drop in the number of new muni bond issues during its fiscal year.

Issuance of long-term debt declined 16% during the fiscal year, while its revenue slipped 11.4%.

However, the board notes that new-issue volume “rebounded dramatically” at the start of fiscal 2010 — last fall ­­­— which should help bolster the MSRB’s financial position this year.

In addition, the board last year eliminated new underwriting-fee exemptions for most short-term debt, a move that was expected to bring in an additional $2 million in annual revenue based on last year’s level of short-term issuance.

With the exception of commercial paper, the MSRB now generally charges underwriting fees of three cents per $1,000 par value of bonds and notes.

The report also reveals that the board on Sept. 15 signed a new three-year ­contract with its executive director, ­Lynnette Hotchkiss, extending her employment until at least the end of fiscal 2012. Her original contract was due to expire in May 2010.

Among the board’s assets, the value of its investments, mostly Treasury securities, declined to $18.24 million from $23.68 million during the fiscal year. Accounts receivable were up to $3.69 million from $2.66 million, while cash rose to $1.47 million from $1.18 million.

The decline in assets came as the MSRB’s liabilities rose to $4.39 million from $3.88 million.

The rise was partly attributable to separation agreements the board entered into in 2009 with three unnamed former employees that entail payments totaling $139,316 over the next year, plus an additional liability of $57,360 for an unnamed employee who was fired during 2009. Sources said the terminated employee had been at the board for several years but was not in senior management.

The MSRB also revealed that it continues to pay medical benefits to former executive director Christopher “Kit” Taylor and his spouse under an agreement that ends in December 2012. The expense appears to total about $102,000 annually.

While overall revenue declined to $19.63 million from $22.15 million, total expenses rose to $21.28 million from $18.56 million, led by costs associated with the development of the board’s Electronic Municipal Market Access, or EMMA, site.

Specifically, the board reported that expenses tied to its “market information transparency programs and operations” had jumped to $10.07 million from $7.22 million.

The expenses reflect the fact that EMMA now provides data on variable-rate securities, all-electronic official statements, and continuing disclosures — programs that were all implemented in fiscal 2009, MSRB chief financial officer Melanie Richardson said in a statement.

Meanwhile, the decline in new-issue underwriting fees was not the only contributor to the decline in revenue, as the board’s investment returns were also down sharply compared to the previous year. Specifically, the MSRB made just $533,667 on its investments in fiscal 2009, compared to $1.12 million the year before.

Transaction fees also fell to $7.15 million from $7.72 million, while annual fees declined to $622,700 from $644,864. The board charges one-half cent per $1,000 par value of most bonds traded.

Data subscriber fees were up to $441,392 from $390,210, initial fees fell to $8,400 from $8,800, and “other income” declined to $29,757 from $67,668. Revenue from manuals fell to $3,511 from $4,526.

The board charges a variety of different subscriptions for its data and in August raised its annual fee for member firms to $500 from $300.

The annual report provides new market statistics. In all of 2009, the MSRB collected data on more than 10 million muni transactions totaling close to $3.8 trillion.

Perhaps underscoring the size of the short-term market, the MSRB said it had collected data from an average of 3,000 auction-rate securities resets each month, with 82% percent being reset at the maximum, or fail, rate.

Meanwhile, the number of variable-rate demand obligation interest rate resets has averaged more than 90,000 per month.

The board unveiled the first phase of its transparency system for auction-rate securities on Jan. 30 and for variable-rate demand obligations on April 30.

It is soon expected to unveil the second and final phases of the system, which collect and display program documents as well as provide Treasury-like details about auctions and remarketings.