The country's interior ministry said Sunday that 2,545 of the attacks were carried out against individual migrants, while 988 targeted places that housed migrants.
The data shows there were over 420 physical attacks and nearly 750 acts of arson and property damage. There were also around 1,380 verbal attacks that included everything from insults to inciting hate speech.
Authorities say the preliminary 2016 figures, along with data from previous years, demonstrate an increasing trend of attacks towards migrants.
The preliminary figures were released in response to a parliamentary question. Final figures are expected to be released in May. According to the ministry, 560 asylum seekers and refugees were injured in the attacks -- 43 children among them.
There were also 217 attacks on refugee organizations and volunteers.
Germany has accepted hundreds of thousands of refugees in the past couple of years, many from war-torn Syria. In 2016, 280,00 migrants applied for asylum in the country. The largest group of applicants come from Syria, Afghanistan, Iraq, Iran, Eritrea, Albania and Pakistan.
The policy has been polarizing, with some parts of the community unhappy with the influx of refugees.
The numbers released for 2016 show a substantial increase in attacks from the prior year. In 2015, officials recorded 1,031 attacks nationwide against asylum seekers. More than 80% of the reported attacks in 2015 were verbal assaults.
Alongside a breakdown of the figures, the German Interior Minister Heiko Maas tweeted Sunday that the attacks on migrants were attacks on open free society.
'Desperately important to do better'
Amnesty International said the figures showed that Germany desperately needed to improve its response to hate crimes.
"Amnesty International published in-depth research last year that warned that there are shortcomings with how Germany prevents and deals with hate crimes," Gauri van Gulik, Amnesty International's deputy Europe director, said.
"These figures show how desperately important it is to do better. We need to see better risk assessments, more protection at certain locations, thorough investigations and prosecutions of these appalling racist attacks to stop them in the future."
In June, the human rights group called for Germany to address what it said were "long-standing and well-documented shortcomings in the response of law enforcement agencies to racial violence."
Its report "Living in insecurity: How Germany is failing victims of racist violence"
said that violent racist crimes had increased by 87% between 2013 and 2015. According to Amnesty, civil society organizations have reported discriminatory identity checks by police on members of ethnic and religious minorities.
Officials with the group said the need to review authorities' responses to hate crimes had taken on "particular urgency" after a rise in such attacks following the arrival of more than 1.1 million new asylum seekers in 2015.
While the asylum seekers had mainly been received with "a welcoming attitude unmatched anywhere in Europe," on average about six anti-refugee protests had been held in Germany every week of that year, Amnesty said.
The group urged the German government to adjust the guidelines on investigating politically motivated crimes "so that an explicit duty is imposed on police to uncover any racist or other discriminatory motive behind criminal offences."
It also called for the development of comprehensive strategies assessing security threats against asylum shelters so that those most at risk of attack could be better protected.
In its annual report released last week,
Amnesty said that the number of racist and xenophobic attacks on asylum shelters in 2016 "remained high and the authorities failed to adopt effective strategies to prevent them."
Germany has been taking steps to tighten its asylum seeker policies,
recently announcing that border controls with Austria -- introduced as a short-term measure in September 2015 -- would continue indefinitely.