The Bazel team is in progress of migrating the native Protobuf rules to Starlark. As a first step towards this goal, starting with Bazel 3.0, all Protobuf rules will require explicit load statements.
You can use the following buildifier command to apply most of the required migrations for you:
buildifier --lint=fix --warnings=native-proto $(find . -name "BUILD" -o -name "BUILD.bazel" -o -name "*.bzl")
For further information, see bazelbuild/bazel#8922 or ping me.
This should be pretty straightfoward to fix, quoting from https://github.com/kythe/kythe/issues/4264 -- the bug Bazel filed against us (Kythe):