However, party spokesperson Renuka Chowdhary hailed the Union minister as a "senior man and seasoned politician".
Congress' apparent soft-pedalling of the issue came a day after SP chief Mulayam Singh Yadav's brother Shivpal Yadav accused Beni of "smuggling opium" and using "charas".
Chowdhary termed the war of words between the SP chief and Beni as "two individuals trading charges against each other."
When the controversy had first erupted with Beni alleging that the SP chief had links with terrorists, Congress had snubbed him saying the party does not share the view and those in public life should speak with decorum.
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Congress President Sonia Gandhi had also told the SP chief that she does not approve of such comments, which brought an end to the controversy.
However, the war words renewed with the Union minister, a few days back, again hitting out at the SP saying that the coming Lok Sabha elections will mark the "funeral procession" of the SP. Shivpal's comment last night saw the controversy hitting a new low.
Chowdhary today said, "We are not commenting on Beni ji as he is a senior man and seasoned politician who knows what he is doing. He can account and answer for what he has to say."
She also evaded a reply when asked whether SP leaders praising L K Advani and the NDA indicate an increasing bonhomie between the two. A section in the party, though, did not discount the possibility of Beni cosying up to BSP. "Ask them" was her brief reply.