A.java

public class A {
}

B.java

public class B {
  com.test.proto.P.Message m;
}

BUILD

proto_library(
    name = "p_proto",
    srcs = ["p.proto"],
)

java_proto_library(
    name = "p_java_proto",
    deps = [":p_proto"],
)

java_library(
    name = "a",
    srcs = ["A.java"],
    deps = [":p_java_proto"],
)

java_library(
    name = "b",
    srcs = ["B.java"],
    deps = [
        ":a",
        ":p_proto",
    ],
)

p.proto

syntax = "proto3";

option java_package = "com.test.proto";
option java_outer_classname = "P";

message Message {
}

WORKSPACE

http_archive(
    name = "com_google_protobuf",
    sha256 = "cef7f1b5a7c5fba672bec2a319246e8feba471f04dcebfe362d55930ee7c1c30",
    strip_prefix = "protobuf-3.5.0",
    urls = ["https://github.com/google/protobuf/archive/v3.5.0.zip"],
)