Ban is in the German city for theinternational conference, where he also met Afghan President Hamid Karzai.
Addressing the media, Ban said Pakistan not attending the crucial meet is "their sovereign decision."
"Pakistan is one of the key countries in the region who can help peace and stability in Afghanistan and thus it would have been much better if Pakistan was present in the conference. I feel it regrettable that Pakistan has decided not to come," Ban was quoted as saying in a statement released by his spokesperson here.
Pakistan's decision to boycott the conference came in the wake of a Nato attack on its border posts that killed 24 of its troops.
The White House and senior Obama administration officials, including secretary of state Hillary Clinton had asked Pakistan to reconsider its decision of not attending the conference.
Ban however added that absence of the Pakistan delegation does not in turn mean that the country will not cooperate in ensuring peace and stability in the South Asian region.
"I am told by German foreign minister Guido Westerwelle that he had been informed by the Pakistani Government that even though they may not be here, the Pakistani Government is committed to fully cooperate with the members of the international community and particularly the Afghan Government to work together and to promote peace and security in the region."
"I believe that Pakistan is committed to work together with the Afghan people and also to promote peace and security in the region and this is mutual interest and you should also have closer cooperation with many Central Asian countries," he said.
The UN chief said he has been emphasising, in his dialogue with leaders from Pakistan and Afghanistan over the years, that both countries should "maintain the neighbourly relationship and closely coordinate and help each other to promote peace and security."
On the UN's role in Afghanistan when the US troops withdraw from the country, Ban said the world body will continue to play a "crucial and even greater" role post-2014.
The United Nations will be responsible during this transitional period and will mobilize its agencies, funds and programmes to provide social and economic help and support the Afghan government in promoting reconciliation and enhancing capacity in good governance.
The UN will focus on eradicating practices like drug trafficking and help establish the rule of law, the secretary general said adding that it will help to ensure the marginalised and vulnerable people, particularly women and girls, live with dignity and respect in the country.