Khan had told PTI last week that he was coming to India to meet the newly elected office-bearers at BCCI including president Jagmohan Dalmiya with focus on revival of cricketing ties between the two neighbours.
However, Thakur said it was just a courtesy meeting."It was a courtesy meeting and we emphasised on continuing the good and cordial relation the two boards and the neighbours," said Thakur on the interaction that took place yesterday evening.
Khan on his part said: "I wanted to convey my best wishes (to the newly elected body) and hope our fruitful discussions will strengthen our ties".
According to the 'binding agreement' signed between the two boards, India and Pakistan are scheduled to play 12 Tests, 30 ODIs and 11 Twenty20s spread over six series with the first one scheduled from December 2015. However, all series will be played subject to Indian government clearance.
The arch-rivals last played a bilateral series in December 2012-January 2013 when Pakistan toured India for a short series.
Pakistan have not played on home soil since the terrorist attack on the touring Sri Lanka team bus in Lahore in 2009.
"The priority is that what we should confirm the MoU that have been signed between the two boards to play six series in eight years and the first will be Pakistan's home series that will be played in the UAE," Khan had said ahead of his India visit.