There is four different cases, one for rooted device, one for emulator, one for regular device and one for rooted or regular device.
On rooted device I was able to get it working so:
In adb:
adb shell
In launched after this shell:
su
stop
setprop dalvik.vm.checkjni true
start
After this device was rebooted and at boot I see log message:
CheckJNI is ON
For other cases see some theory from official docs:
There are several ways to enable CheckJNI.
If you’re using the emulator, CheckJNI is on by default.
If you have a rooted device, you can use the following sequence of commands to restart the runtime with CheckJNI enabled:
adb shell stop
adb shell setprop dalvik.vm.checkjni true
adb shell start
In either of these cases, you’ll see something like this in your logcat output when the runtime starts:
D AndroidRuntime: CheckJNI is ON
If you have a regular device, you can use the following command:
adb shell setprop debug.checkjni 1
This won’t affect already-running apps, but any app launched from that point on will have CheckJNI enabled. (Change the property to any other value or simply rebooting will disable CheckJNI again.) In this case, you’ll see something like this in your logcat output the next time an app starts:
D Late-enabling CheckJNI
You can also set the android:debuggable attribute in your application's manifest to turn on CheckJNI just for your app. Note that the Android build tools will do this automatically for certain build types.