"We are all upset at these events. The government had no role in this that I am sure of. We will find out the details. This should not have...(happened). The timing of the raid is most unfortunate," Singh told reporters here.
The Prime Minister's remarks came even as the searches carried out just two days after DMK pulled out of UPA, triggered a political controversy over its timing with even top central ministers strongly disapproving of the action.
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Congress ministers in UPA including P Chidambaram, Kapil Sibal and Kamal Nath strongly disapproved of the CBI searches, as the Centre distanced itself from the action, saying it was not aware of it.
DMK, which pulled out of UPA on Tuesday and withdrew its ministers yesterday, said the action was a "political vendetta" amid reports that the agency concluded its searches after the uproar broke out.
Searches were carried out at 19 places across Tamil Nadu, including at Stalin's residence in Chennai, this morning in a case of alleged tax evasion of imported cars.
Stalin (60), considered a political heir to 88-year-old Karunanidhi, dubbed the CBI raid as a 'political vendetta' and said he would face the case legally.
BJP said the CBI action is an example of "blatant" misuse of power by the UPA government for its survival and proves that it uses the probe agency to muffle allies who are walking out of the ruling coalition.
The issue was also raised in Parliament with BJP leader M Venkaiah Naidu alleging that the party which withdrew the support to the UPA Government was raided by CBI and said it meant the government "controlled" CBI.