"The wrap up meeting was held in a cordial atmosphere and the Indian delegation has slight reservations over longer stays in Karachi and Peshawar ... we will consider the matter while finalising the itinerary," Khan said on Sunday.
The three-member delegation is expected to return home on Monday after assessing security and other arrangements for the three Tests and five One-day series.
The Indian Government on Saturday announced their team's first Test tour of Pakistan in almost 15 years would go ahead as scheduled next month after reports suggested the tour would be postponed until after the Parliamentary polls expected from late April.
The itinerary for the tour will be finalised by the Board of Control for Cricket in India (BCCI) after the delegation submits its report, likely by Tuesday.
The proposed itinerary includes a side match in Multan or Lahore, a Test each in Lahore, Peshawar and Karachi with the first One-day in Karachi, two Limited Overs matches in Lahore and the remaining in Rawalpindi and Faisalabad.
The PCB had earlier planned to stage the three-day tour opener in Karachi but shifted the match on the Interior Ministry's recommendations.
Australia and the West Indies refused to play in Pakistan due to security fears after the US-led strikes in neighbouring Afghanistan in 2001.
New Zealand were forced to abandon their tour of Pakistan in 2002 after a bomb blast outside the team hotel in Karachi on the morning of a Test match.
Pakistan last year hosted Bangladesh, South Africa and New Zealand but the last two teams rejected Karachi and Northwest Peshawar city bordering Afghanistan as venues due to security fears.
England was the last foreign team to play a Test in Karachi and a side-game in Peshawar in 2000.
The Southern city of Karachi has a history of ethnic violence and bomb blasts.
BCCI's security team holds wrap-up meeting