Positions in the Minneapolis location will shift to St. Cloud.
CEO Randall Hogan also announced he would step down from his position and take over as chairman of the electrical business group.
The site, which would employ more than 150 Northern Minnesotans, was expected to open in 2018.
The Finnish company will have spent more than $35 million in the last two years on expansions of its U.S. headquarters.
The Federal Trade Commission claimed the merger would create unfair market conditions if Pentair’s switchbox business were not divested.
He added that the layoffs were “very unexpected.”
Both its sales and earnings grew by about 4 percent over the year-ago period, beating Wall Street’s estimations.
Brooklyn Park-based Mocon had $63 million in sales last year.
The company is planning an $11 million expansion and expects to have 70 employees working by the end of the year.