"The remark is disgraceful and unfortunate," Singh told reporters in Parliament when asked to comment on Advani's statement in Lok Sabha.
The BJP leader created a storm in Lok Sabha by dubbing UPA-II as "illegitimate" but withdrew it after strong protests from Congress.
Advani, who came under attack from Congress including its President Sonia Gandhi, later said he was referring to the 2008 confidence vote for which "crores of rupees were spent" to save the government.