Writing in the Sena journal, Thackeray said, "I did not criticise Narendra Modi. My criticism is constructive; I criticised Modi's publicists on Uttarakhand."
"He (Modi) is not our enemy. We have expectations of him and expressed our displeasure,' added Thackeray.
Earlier the Sena had taken a dig at Modi for reportedly rescuing 15,000 Gujaratis from flood-ravaged Uttarkhand over the weekend.
The party also accused Modi of looking after the welfare of the people of only his state, indicating that a prime ministerial aspirant should not take a divisive path.
The Sena said Modi's act of saving his own people could lead to an adverse publicity and boomerang. It praised Maharashtra Chief Minister Prithviraj Chavan, who also visited Dehradun at the hour of crisis.