The firm announced this week that Richard Nanula is leaving to "pursue other opportunities" and that its current vice president of operations Robert Bradway will replace him at the end of an agreed 90-day transition period.
Bradway is appointed as executive vice president and CFO, and will be responsible for Amgen's finance, strategy and investor relations operations, the firm said in a statement.
Nanula's departure comes on the heels of series of setbacks the company has experienced in the last few months, including safety and reimbursement issues surrounding two of its leading drugs, Epogen (epoetin alfa) and Aranesp (darbepoetin alfa) - both for the treatment of anaemia.
In particular, the way Amgen handled one of the clinical studies for Aranesp - the study was halted in December, but the firm disclosed its failure three months later - has been questioned and an informal Securities and Exchange Commission probe is currently looking into the issue.
Sparking the crisis, which is being seen by analysts as potentially the biggest one in the company's recent history, were safety concerns about the two anaemia blockbusters - which together generate half of the company's $13.9bn (€10.4bn) 2006 sales.
Recent evidence shows that Aranesp and Epogen pose higher risks of heart attack, stroke and death, which have prompted the US Food and Drug Administration (FDA) to add additional warnings on Amgen's drugs.
In addition, Amgen has come under scrutiny from the US Congress for what it charges patients covered by the government's Medicare insurance programme for the elderly for both Aranesp and Epogen.
Furthermore, Nanula's exit comes just a week after Amgen announced its plans to delay construction of its major new manufacturing plant in Cork, Ireland, part of a $1bn expansion programme announced last year.
Originally due to become operational in 2009, the manufacturing facility will now be several years behind the original schedule, following a "global assessment" of manufacturing needs.
Last month, the company suffered a heavy blow to its pipeline after one of its key new products, Vectibix (panitumumab), failed a late-stage trial as a first-line treatment for colovectal cancer.
Amgen, the world's largest biotech company, is expected to announce its first quarter results next week.