"One of the things that's holding us back is absence of FTA so we pushed pretty hard on that," Key said.
Key said the talks were "very productive" and that Mukherjee conceded that the absence of the FTA was holding back the relationship between the countries.
"I believe an FTA would be a win-win for both countries," said Key.
He said India's demographics were similar to China, New Zealand's biggest trading partner.
"India has huge ambitions to improve its industry and we want to partner with them on achieving just this. In our experience, investment follows trade," he said.
Key said two-way trade between the countries was worth $2.2 billion in 2015 and that India was New Zealand's 10th largest trading partner.
"We see opportunities for collaboration in education and skills development, tourism, energy, clean technology, agri-tech, defence cyber security and ICT," Key said.
Key is also due to meet with French Prime Minister Manuel Valls tonight and said that the European republic plays a big part in whether or not free-trade negotiations get over the line on the continent.
One of the big points Key said he would try to make is that a FTA doesn't mean that New Zealand would "run over" France's agricultural sector.