That position was a huge winner in the first half of 2015, but started to falter in recent weeks, and was pummeled after the Citron report.
Valeant is down 20.15 percent this year.
Ackman's position is now about $1.8 billion in the red since it was acquired, according to the investor.
Less than three years ago, it was Ackman who accused a company of fraud, placing a $1 billion short bet against nutrition and supplements company Herbalife and saying it runs a pyramid scheme, something Herbalife denies.
Herbalife is up about 48 percent this year to around $55.60 a share, further hurting Ackman's portfolio.
Ackman scored a 40 percent gain in 2014 thanks to a huge win on Botox maker Allergan.