In a statement on the eve of a major shareholders' meeting in which YUKOS is merging with a smaller rival Sibneft, the prosecutor general's office said the searches were carried on Wednesday.
YUKOS's former chief Mikhail Khodorkovsky is in jail, after being arrested last month on charges of tax evasion and fraud.
On Thursday, prosecutors said Khodorkovsky, considered Russia's richest man, faced charges on 11 counts. The latest addition to the list was the theft of $2.8 million in proceeds from fertilizer sales.
The charges carry a maximum sentence of 10 years in jail and confiscation of property.
Prosecutors also said that documents from the office of YUKOS-Moscow, a parent company of YUKOS, have been seized during the latest searches.
Many view the crackdown on YUKOS as political vendetta by Russian President Vladimir Putin, since Khodorkovsky funded his political opponents.
Khodorkovsky's arrest triggered global consternation and Russian stock markets plunged in its immediate aftermath.
Prosecutors say Khodorkovsky can stand trial as soon as his lawyers complete studying a 40,000 page document on his case.
Khodorkovsky quit as YUKOS chief after being sent to prison.