Chelsea Manning, the US soldier convicted of transmitting hundreds of thousands of state secrets to WikiLeaks, has formally appealed to President Obama to have her 35-year sentence commuted.

The army private, 25, formerly known as Bradley Manning, has written to Obama and the secretary of the army, John McHugh, asking to be granted a pardon or for her sentence to be reduced to the more than three years' time served. In a statement, which the soldier already made public following last month's sentencing, Manning said her decision to leak to Julian Assange's anti-secrecy group was "made out of a concern for my country and the world that we live in … It was never my intent to hurt anyone. I only wanted to help people."

In a covering letter to the pardon, Manning's civilian lawyer David Coombs adds a harder note, criticising his client's 35-year sentence as one that "grossly exaggerates the seriousness of his conduct. The sentence was disproportionate to both the offense and the offender. It will undoubtedly have a chilling effect on future whistleblowers and damage the public's perception of military justice."

Manning was last month acquitted of the most serious charge against him – that he "aided the enemy" – but convicted of 20 counts relating to the gigantic stash of state secrets she transmitted to WikiLeaks. The files included hundreds of thousands of US diplomatic cables from embassies around the world, war logs from Afghanistan and Iraq and files on Guantánamo detainees.

Manning is beginning her sentence at Fort Leavenworth in Kansas where Coombs said she is doing well. Shortly after she was sentenced, the lawyer revealed that she wanted to live as a woman and change her name from Bradley to Chelsea.

She is requesting hormone treatment in line with general medical care for people with gender dysphoria and has offered to pay for the drugs herself. So far, her military captors have indicated they have no intention of facilitating such treatment.

According to Coombs, unless Manning's request for a pardon is successful the earliest she could be paroled would be after 10 years. The lawyer writes in his covering letter: "We rely upon whistleblowers, even in those instances that might cause embarrassment, to keep our government accountable to its people. Private Manning is a military whistleblower. He disclosed documents that were vital for a healthy public debate about our conduct in Iraq and Afghanistan, our detention policies at Guantánamo, and our diplomatic activities around the world."

In the pardon request, Manning writes: "I will serve my time knowing that sometimes you have to pay a heavy price to live in a free society. I will gladly pay that price if it means we could have a country that is truly conceived in liberty and dedicated to the proposition that all women and men are created equal."