The pipeline and infrastructure company, which has operations in Western Canada and Europe, said it took a $349 million non-cash charge related to the "internalization" of Inter Pipeline's external management contract.
For the quarter ended June 30, the loss amounted to $1.02 per unit compared with a profit of $106.8 million or 39 cents per share a year ago.
Revenue for the quarter totalled $320.3 million, up from $279.9 million in the second quarter of 2012.
Excluding the non-recurring charge, Inter Pipeline said it earned $67 million in its latest quarter.
Funds from operations were $105.4 million or 37 per unit, compared with $110.1 million or 41 cents per unit in the second quarter of 2012.
Inter Pipeline is in the midst of converting from a limited partnership to a corporate structure.
The company has purchased its general partner as part of a move that will eliminate future management, acquisition, and divestiture and incentive fees payable to an external manager.
Unitholders are expected to vote on the second step at a meeting on Aug. 22 in Calgary.
Inter Pipeline owns and operates pipelines, bulk liquid storage and natural gas liquids extraction operations in Western Canada, the United Kingdom, Denmark, Germany and Ireland.