The move will come as a blow to campaigners, including the British Medical Association (BMA), who have been calling for charges to be scrapped altogether.
The Department of Health has also announced that dental charges will rise.
England is the only part of the UK still charging for prescriptions. They are free in Wales and Northern Ireland and will be free in Scotland from April 1.
The NHS in England nets more than £450 million a year from prescription charges.
Last year, the coalition shelved a report ordered by the previous Government into how charges for patients could be reduced.
The study, from Professor Ian Gilmore, former president of the Royal College of Physicians, said the current system of charges was "outdated and arbitrary".
He said all patients with long-term conditions lasting at least six months should be exempt, with the exemption remaining in place for three years.
Patients could then return to their GP to have the exemption period renewed, and ministers should consider scrapping prescription charges altogether for everyone, the report said.
Under today's announcement, the cost of an annual pre-payment certificate will remain at £104, but will rise to £29.10 for a three month certificate.
Dental charge for a band one course of treatment, such as a check-up, will increase by 50p from £16.50 to £17.
A band two course of treatment, including fillings and a root canal, will increase by £1.40, from £45.60 to £47.
Band three treatment, such as dentures and bridges, will increase by £6 from £198 to £204.
Charges for elastic stockings and tights, wigs and fabric supports supplied by hospitals will be also be increased.
A spokeswoman for the Department of Health said the Government was investing an extra £10.7 billion in the NHS and releasing £1.7 billion by cutting bureaucracy.
"The extensive exemption arrangements we have in place mean that in England, around 90% of prescription items are already dispensed free of charge.
"The price of the 12 month prescription pre-payment certificate will be frozen for the second year running. This allows people to get all the prescriptions they need for an average cost of £2 per week.
"Abolishing prescription charges in England would leave the NHS with a funding gap of over £450 million each year.
"This is valuable income - equivalent to the salary costs of nearly 18,000 nurses, or 15,000 midwives, or over 3,500 hospital consultants. This income helps the NHS to maintain vital services for patients."
Sue Sharpe, chief executive of the Pharmaceutical Services Negotiating Committee, which represents community pharmacies in England and Wales, said it was "disappointed" and called for charges to be abolished.
"This rise will mean that people on low incomes, who are unlucky enough to fall ill, may be unable to afford the medication they need. This could damage their health in the long term, and prove pricier for the NHS.
"Pharmacists already see some patients having to make difficult choices about their prescription medicines because they can't afford the charge.
"This is unacceptable, but we're only going to see more of it now."
She said the system was also "overly bureaucratic and expensive" for community pharmacies to process.
"No-one can dispute that the Government needs to make savings to the public purse.
"But increasing the prescription charge increases unfairness and hits the most vulnerable the hardest.
"It's time for England to follow the example of other parts of the UK; it's time for the charge to be abolished."
Nanette Kerr, director of pharmacy at the National Pharmacy Association, said: "We are disappointed with the increase.
"Prescription charges deter many people from getting medicines which their doctor prescribes.
"Patients on low fixed incomes who do not qualify for exemption suffer the most."
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