The Rs 400 crore structure, almost a replica of the state Secretariat Vidhana Soudha in Bangalore, is seen as a step to take state administration closer to north Karnataka region in a bid to assuage the feeling of neglect by the people there.
"I hope the representatives of the region will utilise the new platform provided for good governance, economic growth and to remove regional imbalance," Mukherjee said.
NCP and Shiv Sena had appealed to the President not to inaugurate the Soudha, saying it would mean the Centre was ignoring their state's rights over "Marathi-dominated areas".
The location of the building, housing Assembly, Council besides the secretariat, in Belgaum is considered significant as it is viewed as a symbolic assertion of Karnataka's long-held stand that the city is its integral part.
Maharashtra claims that Belgaum belongs to it but Karnataka has been insisting that it became a closed chapter when the central-government appointed Mahajan Commission in its report in August 1967 had stated that the city was part of Karnataka.
Mukherjee said he was privileged to be amongst people of north Karnataka who had witnessed historic moments in Indian freedom movement from Rani Kittur Channamma fighting against colonial exploitation to Bal Gangadhar Tilak launching 'Home Rule' movement with his slogan "Swaraj is my birthright".
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He also reminisced the holding of Indian National Congress meetings here under the presidentship of Mahatma Gandhi.
Chief Minister Jagadish Shettar assured that the winter session of Karnataka Assembly will be held here every year and committee meetings, cabinet meetings and international conferences will also be held.
Elaborate security arrangements had been made in view of protests by pro-Maharashtra outfits including Maharashtra Ekikaran Samiti against Mukherjee's visit, but police said no protests were held across the district.