Speaking at a press conference to launch the Crown Prosecution Service annual report, she said it was important to avoid putting pressure on innocent defendants to plead guilty.
However, she urged the Royal Commission on Criminal Justice to consider a system whereby judges would offer lower sentences in return for guilty pleas.
Last month, the Bar Council called for formal plea bargaining to be introduced. An informal system already exists, lawyers say, but judges are not allowed to state what discounts can be expected.
Mrs Mills also said ministers should bring in legislation on the disclosure of prosecution evidence to the defence. Her remarks follow Judith Ward's appeal hearing, when the Court of Appeal was highly critical of the prosecution's failure to tell the defence of important evidence at her 1974 trial.
The report showed that three out of four acquittals at crown courts were by jury verdicts, while the rest were on the direction of the judge. Defendants had a 50 per cent chance of acquittal if they pleaded not guilty, Mrs Mills said. The conviction rate in crown courts was 91 per cent and in magistrates' courts 97 per cent, with most of the 1.5 million people prosecuted last year pleading guilty.