The city was rocked by a violent anti-toll agitation recently.
The order was passed by a division bench headed by Justice Abhay Oka.
Three petitions had been filed by Kolhapur residents challenging the toll collection by IRB at nine entry points.
Legal sources said that High Court's decision to stop the toll collection on account of incomplete works may impact toll projects elsewhere in the state.
The Court was informed that an independent consultant had certified that 95 per cent of the work was complete, following which the government issued a notification authorising IRB to collect toll from December 2011.
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Petitioners also argued that section 20 of the Bombay Motor Vehicles Tax Act provides that before levying toll, the state government has to prepare a capital outlay of the project which takes into account factors such as the revenue earning capacity, vehicular movement etc.
No such capital outlay was made. Instead, the government prepared a table of expenditure which did not justify levy of toll, argued Kolhapur Municipal Corporation's lawyer S S Patwardhan. The civic body too is opposing toll collection.
The petitions were today admitted for final hearing, which would take place in due course.