Though its workforce fell slightly to 9,018 the wage bill had gone up 21 percent from a year earlier to 5.2 billion rupees.
The agency had to curb water losses, the Treasury report said.
"The water board is faced with the challenge of ensuring a continuous supply of safe drinking water while enhancing its coverage of providing water to 94 percent of the country by 2016," the finance ministrysaid.
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"As such the Board will have to devise strategies to sustain a capital investment programme with minimum dependence on the government while overcoming the high system losses which will increase productivity."
The report did not mention the reasons for water losses, but earlier media reports had pointed to water piracy and also unmetered connections given to under-served settlements.
Last year Sri Lanka's National Water Supply and Drainage Board had written down assets by 12.6 billion rupe