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Ackman, whose Pershing Square Capital Management owned 5.8 million United Technologies shares at the end of the first quarter, said in a letter that the tie-up is ill-advised. Ackman had previously encouraged United Technologies to streamline its business by splitting up parts of the conglomerate.
The fund manager sent a letter to United CEO Greg Hayes on Sunday morning following a report that the company was in merger talks with Raytheon, the source confirmed to CNBC. Pershing Square declined to comment on the letter.
In a statement to CNBC, United Technologies said, "We are confident that our shareholders will see the merits of this transaction and the value it brings to them and the company. We will be working diligently in the days and weeks ahead to make sure that the details of the transaction are presented to and fully understood by all shareholders."
The Wall Street Journal first reported Ackman's opposition.
Shares of both companies were little changed in after-hours trade Tuesday.
On Sunday, Raytheon and United Technologies announced they would merge in an all-stock deal to create a new company they plan to call Raytheon Technologies. The companies have combined sales of $74 billion annually. That would make the new company the second-largest aerospace and defense company in the U.S. by revenue, behind Boeing.
"By joining forces, we will have unsurpassed technology and expanded R&D capabilities that will allow us to invest through business cycles and address our customers' highest priorities," Hayes, who is set to become CEO of the combined company, said in the announcement.
— CNBC's Leslie Josephs and Christine Wang contributed to this report.