The high-profile probe is part of increased efforts by Kiev's Western-backed leaders to choke off the insurgents' resources and force them to become an even bigger drain on Russia -- whose own economy is undergoing severe stress.
Moscow flatly denies partially bankrolling the guerrillas' 13-month uprising or supporting them with troops and tanks.
But Ukraine's financial battle has secured the support of Western states. The accounts of rebel leaders and top Russian officials believed to be orchestrating their campaign have been frozen in the United States and EU nations since last year and may remain so for the coming months.
Ukraine refers to the war as an "anti-terrorist operation" and prohibits financial or other links with the political chiefs or field commanders of the self-proclaimed Lugansk and Donetsk "people's republics".
SBU spokeswoman Olena Gitlyanska said authorities had no problems with the bank itself.
But UniCredit's Ukrainian office complained that the bank had been cooperating closely with the security service and saw no reason why investigators would effectively shut it down for a part of the day.
"However, SBU agents decided to block our branches' operations by restricting the movement of its personnel, and through other measures."
A Kiev district court last Wednesday allowed the SBU to seize documents of at least five firms suspected of being shells established to hide the identities of those paying the guerrillas' wages and recruiting new troops from Russia's volatile North Caucasus.
The decision immediately gained political dimensions because of the undeclared war that recently broke out between Kiev's year-old leadership and some of the ex-Soviet country's most powerful businessmen.
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