Mark Thompson wrote in a blog that the BBC had seen "disturbing new tactics", including the targeting of family members of those working outside Iran.
Last week, the sister of a BBC Persian staff member was detained and held in solitary confinement at a Tehran jail.
Iran accused the BBC of inciting unrest after the disputed re-election of President Mahmoud Ahmadinejad in 2009.
BBC Persian broadcast online videos and interviewed protesters, who described deaths, injuries and arbitrary arrests carried out by security forces.
In his blog, Mr Thompson wrote that for BBC Persian staff, "interference and harassment from the Iranian authorities has become a challenging fact of life".
"In recent months, we have witnessed increased levels of intimidation alongside disturbing new tactics," he added.
"This includes an attempt to put pressure on those who work for BBC Persian outside Iran, by targeting family members who still live inside the country."
Mr Thompson revealed that last week the sister of a BBC Persian member of staff was arrested and held in solitary confinement on unspecified charges at Evin Prison in the capital, Tehran.
"Although she has now been released on bail, her treatment was utterly deplorable and we condemn it in the strongest possible terms."
Human Rights Watch said that at one point, a man claiming to be the relative's interrogator at Evin telephoned the staff member in London and offered to release her in return for information about the BBC.
Mr Thompson said staff had also faced false accusations of sexual assault, drug trafficking and financial crimes.
In recent months, a number of relatives of BBC Persian staff had been detained for short periods of time by the Iranian authorities and urged to get their relatives in London to either stop working for the BBC, or to "co-operate" with Iranian intelligence officials, Mr Thompson said.
In other instances, passports of family members have been confiscated, preventing them from leaving Iran, he added.
"This has left many BBC Persian staff too afraid to return to the country, even to visit sick or elderly relatives."
He said some had also had their Facebook and email accounts hacked, and been subjected to a "consistent stream of false and slanderous accusations... in the official Iranian media, ranging from allegations of serious sexual assault, drug trafficking, and criminal financial behaviour".
Some reports claimed they had converted from Islam to Christianity or Bahai faith - potentially a capital offence in Iran as it is considered to be apostasy.
Human Rights Watch's Middle East director, Sarah Leah Whitson, said the actions of the Iranian authorities suggested they were attempting to silence reporters and the BBC, and were sending "a message that the government's long arm of repression can extend well beyond borders".
UK Middle East Minister Alistair Burt said Iranian officials' "deplorable tactics illustrate again the deteriorating human rights situation in Iran, and the desperation of the Iranian regime to silence any independent voices".

Helen Smith, who lives in Deal with her British husband and their two children, applied for a new visa last September.
But she is still waiting for officials to return her passport, and said her plea to speed up the process after her grandfather's death was rejected.
UKBA said applicants could not be given updates within the first six months.
Mrs Smith said not being able to attend her grandfather's funeral had been "devastating".
"You've got the support of your family but you just want to be there with them and go through the whole grief and saying goodbye with them," she said.
She had sent a fax to the Border Agency outlining the situation, but did not receive a reply.
Her husband, Ross Smith, said: "I expected an answer that day because of the severity of what had happened - somebody had actually died.
"So somebody must've picked that fax up... and we got nothing, so that was as low as it gets in my eyes."
Charlie Elphicke, the Conservative MP for Dover and Deal, said he was taking up Mrs Smith's case with the immigration minister.
"In cases like this, clearly it should be fast-tracked and what they need to do is take a more risk-based approach," he said.
The UKBA website informs applicants that "you do not need to contact us to check the progress of your application".
"We will contact you as soon as a decision has been made or if we require further information.
"Our staff cannot provide any information about your application if you applied less than six months ago."
Mrs Smith said she was still hoping to fly to New Zealand for the scattering of her grandfather's ashes.
The BBC's director general has accused the Iranian authorities of intimidating those working for its Persian service.
[NEXT_CONCEPT]
A New Zealand woman living in Kent has claimed the UK Border Agency (UKBA) prevented her from travelling to the funeral of her grandfather in Auckland.