A spokesperson for Los Angeles Superior Court confirmed an arrest warrant for Mr Morgan – who is yet to comment – had been issued.
Lee, who first helped dream up The Fantastic Four for Marvel Comics in 1961 and went on to co-create titles including Spider-Man and The Incredible Hulk, endured faltering eyesight and memory loss towards the end of his life.
His final few months were marred by conflicting claims over who was running his affairs.
New York memorabilia dealer Mr Morgan, 42, became close to Lee after the death of his wife, Joan, who died in 2017, also aged 95.
The charges follow previous filings against Mr Morgan in May and June last year, including falsely reporting an emergency and falsely reporting a crime, along with a probation violation.
This culminated in a judge granting a restraining order brought by Lee’s family, after Mr Morgan was accused of moving the magnate out of his home at midnight to isolate him from his caregivers.