Describing the scene as one of "devastation," Qi Baohe said the flood had soaked more than 200,000 traditional thread-bound books.
A 300-year-old woodcut Dazangjing, a precious Buddhist scripture and one of only three in the country, is among the ruined texts.
Other artefacts damaged by the water include Tibetan carpets and blankets gifted to the central government in the 1950s.
"The staff were busy with repair work today, but it's still hard to estimate the losses considering their tremendous value," an official with the palace told China Daily yesterday.
She refused to explain whether and how losses would be compensated.
Staff at the palace used hairdryers to try and salvage waterlogged books, reports said.
The accident happened at 10 am on Tuesday when a hot water pipe broke, flooding the library and museum underneath the palace's theatre, according to Qi.
Damage to electrical and stage equipment has forced all performances scheduled over the next 20 days to be cancelled, sources with the palace said.
At 4 pm on Tuesday, water in the library storeroom was still more than 10 centimetres deep, the source said.
By 8 pm, the leak had been stopped and the heating system repaired, according to sources with the Beijing District Heating Group.
Together with the Great Hall of the People, the national culture palace was one of the top 10 famous buildings constructed after the founding of New China in 1949.
The palace is in the Xidan downtown area of Beijing's Xicheng District and includes an exhibition hall, a library and an opera theatre.