While foreigners require special permits to visit certain protected areas in India, the domestic tourists also require an ILP in certain regions, not necessarily the same. Here is a short account of these requirements in North East India.
What are Inner Line Permits?
Think of them as a visa that you require to travel within your country. 😬
Started by the Britishers (like most other nuisances), the ILP is a document that limits the stay of an Indian citizen in a “protected area”.
The document is an effort by the government to regulate movement to certain areas located near the international border of India. This is an offshoot of the Bengal Eastern Frontier Regulations, 1873, which protected Crown’s interest in the tea, oil and elephant trade by prohibiting “British subjects” from entering into these “Protected Areas” (to prevent them from establishing any commercial venture that could rival the Crown’s agents). The word “British subjects” was replaced by Citizen of India in 1950. Despite the fact that the ILP was originally created by the British to safeguard their commercial interests, it continues to be used in India, officially to protect tribal cultures in northeastern India. 
While the primary reason for the ILP is to deter the people employed in these areas from settling down in the tribal lands, it is required for domestic tourists as well. Though it is easily granted, getting one can be a nuisance.
Getting the ILP
The easiest way to get an ILP for Arunachal Pradesh is the eILP. The eILP is, as per our experience, granted within a single working day and is super easy as compared to other offlines ways of getting an ILP. Moreover, you can simply choose multiple districts, apply as a group and pay your fees online making this a very straightforward process. The ILP is granted for a period of 30 days at a time.
In case you are hell bent on making your life difficult, you can apply for an ILP offline in any of the locations mentioned on the Arunachal Tourism website.
All things said and done, we found the Arunachal ILP to be the easiest to procure.
The ILP checkpoints exist at various places in Arunachal Pradesh. It is usually at the entry-point to the state from somewhere in Assam and would change depending on which sector and district you are going to. Ideally they are also located at the district borders.
In our experience, the ILP checks are somewhat random. The route to Tawang was probably the most strict about ILP and we were asked to sumbit a copy at the Bhalukpong gate. We were also asked for ILP by our hotels in Tawang. On some other gates, we stopped to get them check on our own accord and were waved off by the police 😶 But do carry it at all times, even when going on day trips around your base location.
Getting the ILP
Unfortunately the ILP for Nagaland is not as simple as the eILP of Arunachal. They do have an online portal but it seems redundant, at least at this point of time. To get an ILP you need to apply offline. If you can, apply at the Nagaland House in these cities :
Since Dimapur does not (currently) require an ILP, you can also apply at the office of the Deputy Commissoner in Dimapur. This requires extra effort and a lot of patience though!
Another easy way to apply, in case you have your travel prearranged, is through your hotel in Kohima or Dimapur, or the travel agent that you are booking your Nagaland travel with.
It is reported that the Naga authorities demand ILP at any random location. This is however very erratic. In our experience, we were not asked for the ILP once in our travel. But once again, this being a sensitive area, do carry your ILP with you at all times.
Manipur currently does not require an ILP. However, there is an increasing demand from the locals to bring the state under ILP restrictions. Read here and here in case you are interested to know more.
However, if you are reaching Manipur via Nagaland, you will require a valid Nagaland ILP (see above).
Getting the ILP
Mizoram ILP can be applied offline at Mizoram House in the following cities :
We do not have any experience (yet) regarding the ILP application procedure but it should be easy enough to get a tourist ILP.
Once again, from hearsay, we know that Mizoram has strict checking of ILPs. Expect to show your ILP when crossing over to Mizoram from any of the bordering states.