X-ray machines will be installed, as well as explosive-detecting sensors, the paper reported.
Lynch also told the newspaper: "We've got a major problem with Iranian munitions streaming into Iraq. This Iranian interference is troubling and we have to stop it."
The base will be about four miles from the Iranian border and will be used for at least two years.
US officials told the paper that it is unclear whether it will be among the small number of facilities that would remain in Iraq after any future withdrawal by the US military.
The report comes on the same day as General David Petraeus, the highest-ranking US commander in Iraq and Ryan Crocker, the US ambassador to Iraq, present a report to the US congress on the war.
Jonathan Withington, a Pentagon spokesman, told Reuters news agency that he could not comment on the specifics of the planned base, but said that "coalition and Iraqi partners will continue to put pressure on the enemy, including disruptions of any supply lines, in an effort to reduce violence and to protect the Iraqi people".
Major Toby Logsdon, a US officer overseeing the project, said the new base will have living quarters for at least 200 soldiers, who could arrive in November.
Logsdon said: "Iran will know this is here - they will have to rethink how they do things, and the smugglers will have to rethink how they do things."
US officials accuse Iran of fomenting violence to destabilise Iraq and of seeking to build nuclear weapons under the cover of a civilian nuclear programme, charges Iran has denied.