The former chief inspector of prisons Dame Anne Owers has been appointed to lead the independent police watchdog.

The appointment comes after nearly two years in which the Independent Police Complaints Commission (IPCC) has been without a permanent chairperson, and at a time when the organisation is involved in several high-profile investigations.

Dame Anne Owers, who was chief inspector of prisons from 2001 to 2010, said: "I am delighted to be joining the IPCC at this exciting time of change and challenge for the commission and the police service.

"The IPCC's independent investigation and oversight plays a critical role in ensuring public confidence in policing, and I look forward to working with the commissioners and staff as they continue to carry it out."

While chief inspector of prisons, Dame Anne Owers gained a formidable reputation and produced a series of hard-hitting, critical reports. She has recently been carrying out an inquiry into the reorganisation of the Northern Ireland prison service. She labelled the system in Northern Ireland "dysfunctional, demoralised and ineffective", in a report last October judged by justice ministers as a "watershed".

The appointment of the new chair comes after months in which the IPCC has seemed at times rudderless, with some insiders complaining of a lack of leadership. The last permanent chair, Nick Hardwick, left in April last year, and since then the organisation has faced some of its biggest challenges.

It is currently involved in an independent inquiry into the fatal shooting of Mark Duggan last August, which sparked the summer riots. It is also supervising Operation Elveden, the Metropolitan police's investigation into alleged police bribes – an inquiry that has seen it exercise its powers of arrest.

Dame Anne Owers's appointment amounts to a straight – albeit very protracted – job swap with the former IPCC chair Hardwick, who took over as chief inspector of prisons in 2010 following his departure from the police watchdog.

It is believed that several other candidates were interviewed and rejected last summer. A second interview process in the autumn with a fresh set of candidates was carried out, but there were still long delays before any announcement by the home secretary could be made.

Dame Anne Owers will take an annual salary of £60,000 for the part-time role.

The home secretary, Theresa May, said Dame Anne Owers "has considerable experience of criminal justice and a formidable public reputation".

As IPCC chair she would "challenge all parties to get to the truth and ensure that the organisation provides a fair, transparent and trusted service to the public and police", May said.

Jane Furniss, the IPCC's chief executive, said: "Dame Anne Owers' experience of leading organisations based on independence could not be stronger.

"This, coupled with her wealth of knowledge from across the criminal justice system makes for an exciting new era for the IPCC.

"I welcome the appointment and very much look forward to working with her to build upon the last eight years and take the work of the IPCC forward."

Deborah Glass, the deputy chairwoman of the IPCC, added: "This is timely, with the recently launched review of the way that we investigate our most serious cases, the work we are doing on police corruption and the increasingly high number of independent investigations we are conducting."

Dame Anne Owers will take over from the current interim chairman, Len Jackson, and was appointed by the Queen following recommendations from the home secretary and prime minister.

Her strong human rights background includes roles as director of the Joint Council for the Welfare of Immigrants, and co-director of Justice, the UK based human rights and law reform organisation.

Dame Anne Owers was educated at Washington grammar school, County Durham, and at Girton college, Cambridge. On graduating she went to Zambia to teach and to carry out research into African history. While taking time out to bring up her three children, Dame Anne continued to undertake research as well as doing voluntary advice and race relations work.