The Japanese government ruled in September that Takahashi's death had been caused by working excessive hours.
The official is believed to have had Takahashi underreport her overtime hours after having her work beyond the ceiling agreed upon by the company management and the labor union, according to investigative sources.
Reports said Ishii will tender his resignation at a Dentsu board meeting next month but stay in the role until March.
The bulk of inspections, which looked into cases of Dentsu employees' karoshi - death from overwork - as well as work-induced psychological problems, were carried out after June 2014 and before Takahashi's death.
In a separate statement, Dentsu said: "Today a case against Dentsu Inc. and one of its employees in Japan has been referred to the prosecutors office for alleged violations of the Labor Standards Act".
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Work-related stress contributes to some 2,000 suicides a year, according to the government, while other victims die from heart attacks, strokes and other conditions brought on by spending too much time in the office. "We deeply regret failing to prevent the overwork of our new recruit".
Employees working excessive overtime has become endemic in Japan, with a government survey from October stating that one in five Japanese companies have employees who work such long hours that they are at serious risk of death.
Dentsu has been under pressure to reduce the amount of overtime its employees do and in November it was raided by labour regulators. Instead, some experts say that an overhaul in the structuring of Japanese life is needed, emphasizing a shift in values from work to family, hobbies, and activities that can boost the economy as well as ridding the culture of its affinity for long hours. The paper, which itself received a government warning about overtime this month, acknowledged that changing attitudes would be hard but was essential as it affected employee morale and productivity.
She jumped to her death in December a year ago and in a note left for her mother, she asked: "Why do things have to be so hard?"
Ichiro Oshima, 24, didn't get a single day off for 17 months and had averaged less than two hours of sleep a night.