Hi,
Protected Area Permit (PAP) for various places in Sikkim are issued as follows:-
East District:-
Tsongo – Baba Mandir - permit are issued by Police Check Post for Domestic Tourist. Foreign tourist are allowed till Tsongo Lake, permit is issued by Tourism & Civil Aviation Department and Police check post.
Nathula Pass – Permit is issued by Tourism Department and Police Check Post for domestic tourist.
North District:-
Yumthang – Permit is issued by Police check post for Domestic Tourist and for foreigners permit is issued by Tourism Department and Police Check Post
Yumesamdong - Permit is issued by Police check post for Domestic Tourist and for foreigners permit is issued by Tourism Department and Police Check Post
Thangu-Chopta Valley – Permit is issued by Police Check post for Domestic Tourist and for Foreigners permit is issued by Tourism Department and Police check post. Foreigners must apply through a Sikkim Tourism registered Travel Agent in groups of two people or more for visiting these areas.
Gurudongmar – Permit is issued by Police check post for domestic tourist and for foreigners permit is issued by Tourism Department till Thangu.
Green Lake Trekking Permit is issued by Tourism Department after obtaining a valid permit from Ministry of Home Department, New Delhi.
You can find all this information in the government webiste - https://www.sikkimtourism.gov.in/Public/TravellerEssentials/pap