Modi said the inconvenience faced by the citizens was "totally avoidable."
All government and private schools in Chandigarh were on Thursday ordered to be closed for Modi's visit to the city.
During his brief visit, Modi inaugurated the state-of-the-art new civil air terminal building, addressed the 34th Convocation of Postgraduate Institute of Medical Education and Research and a public rally.
Consequently, the parking lot at the main crematorium in the heart of the city was turned into parking space for the public rally. Bereaved families were asked to use another crematorium in the western part of the city.
"The inconvenience caused to citizens in Chandigarh, especially shutting of schools, due to my visit is regretted. It was totally avoidable.
"An inquiry will be held & responsibility will be fixed for the inconvenience caused to the people of Chandigarh," Modi said in two tweets.
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