Government policies on human rights were negatively affected by the end-2014 deadline for the withdrawal of international combat forces and the negotiations over US troop presence after 2014.
Human rights concerns increasingly took centre stage ahead of the planned April 2014 presidential election, it said.
In the 667-page world report, its 24th edition, Human Rights Watch reviewed human rights practices in more than 90 countries.
The Afghan government of President Hamid Karzai made a series of decisions in 2013 that undermined human rights, particularly those of women and girls, the US-based group said.
Taliban insurgents continued their campaign of targeted assassinations of government officials, including women.
Security is of key concern in the run-up to the presidential election, having a particularly harmful effect on the participation of women who already have a severely limited role in Afghan political life.
A string of physical assaults in 2013 against high-profile women, including murders, highlighted the danger to activists and women in public life.
Human Rights Watch research documents declining security and respect for human rights in the country.
Government security forces and other armed groups continue to commit abuses with impunity.
Deteriorating local security and growing fears for the future contributed to increasing numbers of Afghans fleeing their homes for other parts of the country, other countries, or choosing not to return from overseas.
The UN High Commissioner for Refugees documented an increase of more than 106,000 internally displaced people from January to June 2013, bringing the total to over 583,000.
The main causes of displacement were armed conflict and diminished security, the report said.