The plan does not match the "standards" of US presidents over the last 40 years, Walter Shaub said.
A Trump lawyer said earlier the new trust would face "severe restrictions" on new deals.
But Mr Shaub said the plan would not remove conflicts of interest.
"Every president in modern times has taken the strong medicine of divestiture," he said, referring to a process whereby Mr Trump would sell off his corporate assets and put the profits into a blind trust run by an independent trustee.
At a news conference on Wednesday, lawyer Sherri Dillon said that management of the Trump Organization would be transferred to a trust controlled by Mr Trump's sons Don and Eric and chief financial officer Allen Weisselberg.
The Trump Organization is an umbrella company for Donald Trump's hundreds of investments in real estate, brands and other businesses.
Outlining a structure designed by her and colleagues at the law firm Morgan, Lewis & Bockius, Ms Dillon said President-elect Trump wanted Americans to have no doubt that he was "completely isolating himself from his business interests".
The trio in charge "will make decisions for the duration of the presidency without any involvement whatsoever by President-elect Trump", she said.
No foreign deals will be made and domestic deals will be subject to "vigorous vetting", she added.
Soon after, Mr Shaub said that the arrangement would not remove conflicts of interest for Mr Trump since, unlike in a blind trust, he would still see information about the businesses and deals being made in the newspapers and on television.
"His sons are still running the businesses and, of course, he knows what he owns," he said at the Brookings Institution think tank in Washington DC.
"Nothing short of divestiture will resolve these conflicts."
The ethics agency director compared the Trump plan to what he characterised as secretary of state nominee Rex Tillerson's successful efforts to make a "clean break" from Exxon, where he was chairman and chief executive.
"He clearly recognises that public service sometimes comes at a cost," Mr Shaub said of Mr Tillerson.
Although presidents are not subject to the same conflict of interest rules as other government employees, previous commanders-in-chief have placed their investments into a blind trust to prevent any question of corruption.
The Office of Government Ethics is not an enforcement body - it is there to guard against government members being involved in conflicts of interest.
Mr Shaub said the OGE was waiting to assist Mr Trump if he decided to "adjust his plan".
Posted by Amare Asrat