Dame Sally Davies is worried that recent controversies over the use of medicines have damaged faith in the way research is carried out and presented.
The review will publish its findings by the end of the year.
A copy of her request was obtained by the BBC's File on 4 programme as part of an investigation into concerns about a clot-busting treatment for strokes.
The CMO told the Academy of Medical Sciences she was very concerned" about a view that doctors and scientists are "untrustworthy".
She set out her concerns in a letter, sent in February, to the president of the Academy, Prof Sir John Tooke.
In this, she cited recent debates over the use of cholesterol-lowering statin drugs for people at low risk of developing heart disease, and the anti-viral treatment Tamiflu.
The letter reads: "There seems to be a view that doctors over-medicate so it is difficult to trust them, and that clinical scientists are all beset by conflicts of interest from industry funding and are therefore untrustworthy too."
She says this is not in the interests of patients or the public's health.
"I have, therefore, reluctantly come to the conclusion that we do need an authoritative independent report looking at how society should judge the safety and efficacy of drugs as an intervention."
The academy's review, which starts on Wednesday, will also consider the use of the clot-busting stroke treatment alteplase - a technique called thrombolysis.
Each year in the UK, there are more than 150,000 strokes. About 85% are caused by an obstruction blocking the flow of blood to the brain.
Patients with this type of stroke may be eligible for treatment with alteplase, subject to tests in hospital.
File on 4 visited the hyper-acute stroke unit at Salford Royal NHS Foundation Trust to see how staff assessed and administered alteplase.
Dr Jane Molloy, the clinical lead for stroke services, described how they explained the potential benefits to patients and their families.
Doctors would say that for every three people treated with this medication one will make some extra improvement, and one in seven will recover their independence who would not do so otherwise, she said.
They then set out the risks.
"We know that the risk of bleeding with thrombolysis is six in 100 and that will include minor bleeding but also might include major bleeding with the possibility that it could cause a fatal bleed in the brain."
Some doctors say the benefits have been exaggerated. Dr Roger Shinton, a former stroke physician at Birmingham's Heartlands Hospital, is sceptical.
He said: "I'm prepared to accept that there are some patients who could get some benefit, but overall it may be that on balance the number of people benefiting is actually quite small and does not justify the use given the significant harms that we know."
His concerns have won powerful backing from the former president of the Royal College of Physicians, Sir Richard Thompson.
"My worry is that the trials are not consistent, that the evidence is not strong enough to be giving, after all, a very expensive treatment," he said.
"Do we want to recommend a treatment with a marginal effect when we know we are - if you like - killing a few patients and saving others?"
Dr Shinton wants all the trial data on alteplase to be published. Until then, he argues, routine use of the drug for stroke should be suspended.
But Dr Dale Webb, from the Stroke Association, defended the treatment.
He said: "The evidence says that alteplase has made a big impact on the recovery of stroke survivors.
"We have to remember that the number of disabilities associated with stroke is greater than any other medical condition.
"A stroke really can turn your world upside down.
"What alteplase has done is to improve the long-term recovery outcomes for stroke patients."
In a statement, Boeringer Ingelheim - which holds the licence for alteplase in Europe - said its medicine played a vital role in the treatment of acute strokes.
"We are confident in our data, which is supported by the experience of clinicians who have been using our medicine to treat their patients for more than a decade," it said.
"We are incredibly proud of the contribution our medicine makes to patient care at this critical time."
The Medicines and Healthcare products Regulatory Agency is carrying out a review into the safety and efficacy of alteplase.
It says it will publish the findings before the end of the year.