The deal, struck between newsagents and Home Office officials, is not legally binding but trading standards will be able to reprimand offending outlets.
MPs and campaigners had raised concerns about explicit content in so-called "lad mags" and some tabloid newspapers.
The advice being issued to 19,000 newsagents is to display such magazines out of the sight of children.
But the new measures will not specify they should be placed on the top shelf.
The guidelines do not name any magazines but titles such as Loaded, Nuts and Zoo are likely to be included in its remit.
Newspapers such as the Daily Sport can remain on the bottom shelf if they are folded in a way to conceal sexually explicit content.
When I was in Scotland, the lad's mag section is chock full of such titles as Loaded, Front, Nuts, Zoo, Maxim, and FHM. They're not pornographic as such, but are much more explicit than their American counterparts. And they really are displayed all over the place, including Nuts, which is nothing but football, beer, and boobs, which one newsagent sold on the counter right next to the cash register.