The reaction comes a day after Goa Assembly's Deputy Speaker Michael Lobo levelled the allegation after visiting Kanakumbi at the border of Karnataka and Goa with Speaker Pramod Sawant on Monday.
Alleging that the Goa leaders were indulging in mischief, Mr Siddaramaiah said there was "no violation."
"Let them (Goa leaders) say whatever they want to say but there is a tribunal to decide," Mr Siddaramaiah told reporters in Bengaluru.
"The matter is pending before the tribunal. It will decide whether we have violated its order or not. Just because their deputy speaker says so that does not mean that there was a violation," Mr Siddaramaiah said.
At least 45 TMC ft of water originate in Karnataka, he said.
"Nearly 200 TMC water (in the river) straightaway goes to the sea. All that we are asking for is 7.5 TMC, which the Goa leaders are not ready to share," Mr Siddaramaiah said.
Mr Lobo has alleged that there was a total diversion of water from Mahadayi tributary at Kanakumbi by Karnataka government by constructing underwater canals.
"Whatever water is flowing down to Goa from there is just seepage," he has alleged, adding if the diversion was not stopped, the Mahadayi in Goa will run dry.
Mr Lobo has said a resolution against it is likely during the Goa Budget session.
The Mahadayi Water Dispute Tribunal, which is hearing the dispute between Goa and Karnataka over the sharing of the river water, should be asked to inspect the site at Kanakumbi so that it knows the reality, Mr Lobo said.
The dam at Kanakumbi is one of the projects proposed by Karnataka and opposed by Goa.