The DoJ said ValueAct had not fully disclosed its stake in the companies and the influence it had in their business dealings.
It accused ValueAct of using its access to executives at the firms to influence the outcome of the deal.
ValueAct has denied the charges.
ValueAct purchased $2.5bn (Â£1.75bn) worth of shares in oilfield services companies Halliburton and Baker Hughes after the companies announced their $35bn merger plans in 2014.
"ValueAct's substantial stock purchases made it one of the largest shareholders of two competitors in the midst of our antitrust review of the companies' proposed merger, and ValueAct used its position to influence decision-making at both companies," said assistant attorney General Bill Baer.
In a statement, ValueAct said, "We fundamentally disagree with the Department of Justice's allegations in this case."
The merger of Halliburton and Baker Hughes, originally intended to close by the end of last year, has been delayed by antitrust reviews.
The US Justice Department has filed a lawsuit against investment firm ValueAct, alleging it violated anti-competition rules connected to the merger of Halliburton and Baker Hughes.