He also said the GST Council should continuously review the implementation and suggest suitable improvements to the new indirect taxation regime.
"The new era in taxation, which we are about to initiate in a few minutes, is the result of a broad consensus arrived at between the Centre and states," Mukherjee said minutes before the GST rollout in his speech at a special function in the central hall of Parliament.
The President termed the Goods and Service Tax (GST) a disruptive change.
"It is also a moment of some satisfaction for me because, as the Finance Minister, I had introduced the Constitution Amendment Bill on March 22, 2011," he said.
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"It is similar to the introduction of VAT when there was initial resistance. When a change of this magnitude is undertaken, however positive it may be, there are bound to be some teething troubles and difficulties in the initial stages," he said.
"Success of such major changes always depends on their effective implementation. In the months to come, based on the experience of actual implementation, the GST Council and the Central and state governments should continuously review the design and make improvements, in the same constructive spirit as has been displayed till now," he said.
The President said the GST will "also make our exports more competitive and also provide a level playing field to domestic industry to compete with imports."
"Similarly, the hidden effect of cascading means that the total tax incidence on domestic industry is not transparent," he said.
Under GST, Mukherjee said the tax incidence will be transparent, enabling full removal of tax burden on exports and full incidence of domestic taxes on imports.
By creating a unified common national market, the GST will act as a major boost to economic efficiency, tax compliance and domestic and foreign investment, the President said.
Mukherjee recalled the proposal to introduce GST was first mooted in the Budget Speech for the financial year 2006 -07.
He further said, "It is also a moment of some satisfaction for me because as the Finance Minister, I had introduced the Constitution Amendment Bill on March 22, 2011.
"I was closely involved in the design and implementation and had the occasion to meet the Empowered Committee of state finance ministers, formally and informally, as many as 16 times.
He observed that given the magnitude of the task, it was not a surprise that there were many contentious issues.
"Yet, I found both in those meetings and in my many interactions with Chief Ministers, Finance Ministers and officers of states, that most of them had a constructive approach and an underlying commitment to the introduction of GST.
The President said his confidence stood justified when on September 8, 2016, after the Bill was passed by both Houses of Parliament and more than 50 per cent of State Legislatures, he had the privilege of giving assent to the Constitution (One Hundred and First Amendment) Act.