So-called shaken baby syndrome broadly refers to non-accidental injury to an infant resulting from violent shaking.
The guidance updates advice issued five years ago after high profile cases.
Previous advice came after the attorney general ordered a review of all cases in the previous decade which had involved convictions for killing infants aged under two.
It followed concerns over the evidence of the paediatrician Professor Sir Roy Meadow in the Angela Cannings prosecution, which involved sudden infant death, not shaken baby syndrome.
Mrs Cannings was found guilty of smothering her seven-week-old son in 1991 and her 18-week-old son eight years later. These convictions were later overturned.
The Cannings case was one of several which raised concerns that many parents convicted of killing their children were victims of miscarriages of justice.
The judges who released her ruled that no-one should be prosecuted solely on the basis of medical opinion which was disputed between experts.
Sir Roy was later found guilty of serious professional misconduct and struck off the medical register, but was reinstated after an appeal which overturned the GMC's verdicts.
Sir Roy also gave evidence in the case of Donna Anthony who was freed on appeal in 2005 after being imprisoned for life eight years earlier for killing her 11-month-old daughter and four-month-old son.
Her case was one of the 28 referred to the Criminal Cases Review Commission after Mrs Cannings was released.
In its updated guidance, the CPS also urged prosecutors to challenge defence experts who claim the three head injuries generally associated with shaken baby syndrome may be explained by a lack of oxygen, infection, or raised intracranial pressure.The defence experts' theory, known as the "unified hypothesis", was rejected by the Court of Appeal as recently as July, said Ms Squibb-Williams, who is the senior policy adviser in the CPS's strategy and policy directorate.
She said shaken baby syndrome cases were "complex and sensitive cases".
"The guidance makes clear that it is unlikely that a charge for a homicide or attempted murder or assault offence could be justified where the only evidence available is the triad of injuries," she said.
She went on to say that, in cases where the three internal head injuries are found, "the prosecutor will always consider all the surrounding circumstances and the evidence in each case before reaching a decision".
The senior policy adviser added: "Each case will have its own individual facts and very careful consideration will be given in deciding whether there is sufficient evidence for a realistic prospect of conviction, and then in considering whether it is in the public interest to bring a prosecution."