The division bench of Justices S J Vazifdar and G S Patel was hearing a public interest litigation filed by social worker Dattatray Mane and four others from Ichalkaranji, seeking criminal action against the industrial units.
The petition has also sought action against officials of municipal bodies of Ichalkaranji and Kolhapur.
At the last hearing, court had asked the National Environmental Engineering Research Institute (NEERI) to look into the issue and suggest corrective measures.
"The MPCB has to ensure that NEERI has access to all industries in the 45-kilometre stretch of the Panchganga river and catchment area. Needless to say MPCB is bound to take action against errant industries in accordance with law," the court said.
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The court said municipal bodies of Kolhapur and Ichalkaranji would bear the cost of NEERI study.
NEERI's team would also examine if the sewage treatment plant of the Kolhapur Municipal Corporation can deal with the problem as per the norms of MPCB.
Untreated effluents from hundreds of cloth bleaching units in Ichalkaranji, eight major industries including some sugar factories and sewage from 174 villages find their way into the river, but MPCB did not initiate action against the officials the two civic bodies, the petition says.