Currently, with AWS ECS combined with an internal NLB it is impossible to have inter-system communication. Meaning container 1 (on instance 1) -> internal NLB -> container 2 (on instance 1). Because the source IP address does not change and stays the same as the destination address the ECS instance drops this traffic.
I found a thread on the AWS forums here https://forums.aws.amazon.com/message.jspa?messageID=806936#806936 explaining my problem.
I've contacted AWS Support and they stated to have a fix on their roadmap but they cannot tell me when this will be fixed so I am looking into ways to solve it on my own until AWS have fixed it permanently.
It must be fixable by altering the ECS iptables but I have not enough knowledge to completely read their iptables setup and to understand what needs to be changed to fix this.
iptabels-save output:
:DOCKER - [0:0]
:DOCKER-ISOLATION - [0:0]
:DOCKER-USER - [0:0]
-A FORWARD -j DOCKER-USER
-A FORWARD -j DOCKER-ISOLATION
-A FORWARD -o docker0 -m conntrack --ctstate RELATED,ESTABLISHED -j ACCEPT
-A FORWARD -o docker0 -j DOCKER
-A FORWARD -i docker0 ! -o docker0 -j ACCEPT
-A FORWARD -i docker0 -o docker0 -j ACCEPT
-A DOCKER -d 172.17.0.3/32 ! -i docker0 -o docker0 -p tcp -m tcp --dport 5000 -j ACCEPT
-A DOCKER -d 172.17.0.2/32 ! -i docker0 -o docker0 -p tcp -m tcp --dport 5000 -j ACCEPT
-A DOCKER -d 172.17.0.5/32 ! -i docker0 -o docker0 -p tcp -m tcp --dport 8086 -j ACCEPT
-A DOCKER-ISOLATION -j RETURN
-A DOCKER-USER -j RETURN
COMMIT
# Completed on Wed Jan 31 22:19:47 2018
# Generated by iptables-save v1.4.18 on Wed Jan 31 22:19:47 2018
*nat
:PREROUTING ACCEPT [0:0]
:INPUT ACCEPT [0:0]
:OUTPUT ACCEPT [38:2974]
:POSTROUTING ACCEPT [7147:429514]
:DOCKER - [0:0]
-A PREROUTING -m addrtype --dst-type LOCAL -j DOCKER
-A PREROUTING -d 169.254.170.2/32 -p tcp -m tcp --dport 80 -j DNAT --to-destination 127.0.0.1:51679
-A OUTPUT ! -d 127.0.0.0/8 -m addrtype --dst-type LOCAL -j DOCKER
-A OUTPUT -d 169.254.170.2/32 -p tcp -m tcp --dport 80 -j REDIRECT --to-ports 51679
-A POSTROUTING -s 172.17.0.0/16 ! -o docker0 -j MASQUERADE
-A POSTROUTING -s 172.17.0.3/32 -d 172.17.0.3/32 -p tcp -m tcp --dport 5000 -j MASQUERADE
-A POSTROUTING -s 172.17.0.2/32 -d 172.17.0.2/32 -p tcp -m tcp --dport 5000 -j MASQUERADE
-A POSTROUTING -s 172.17.0.5/32 -d 172.17.0.5/32 -p tcp -m tcp --dport 8086 -j MASQUERADE
-A DOCKER -i docker0 -j RETURN
-A DOCKER ! -i docker0 -p tcp -m tcp --dport 32769 -j DNAT --to-destination 172.17.0.3:5000
-A DOCKER ! -i docker0 -p tcp -m tcp --dport 32777 -j DNAT --to-destination 172.17.0.2:5000
-A DOCKER ! -i docker0 -p tcp -m tcp --dport 32792 -j DNAT --to-destination 172.17.0.5:8086
COMMIT
# Completed on Wed Jan 31 22:19:47 2018
ip a:
1: lo: <LOOPBACK,UP,LOWER_UP> mtu 65536 qdisc noqueue state UNKNOWN group default qlen 1
link/loopback 00:00:00:00:00:00 brd 00:00:00:00:00:00
inet 127.0.0.1/8 scope host lo
valid_lft forever preferred_lft forever
inet6 ::1/128 scope host
valid_lft forever preferred_lft forever
2: eth0: <BROADCAST,MULTICAST,UP,LOWER_UP> mtu 9001 qdisc mq state UP group default qlen 1000
link/ether 0a:b4:86:0b:c0:c4 brd ff:ff:ff:ff:ff:ff
inet 10.12.80.181/26 brd 10.12.80.191 scope global eth0
valid_lft forever preferred_lft forever
inet6 fe80::8b4:86ff:fe0b:c0c4/64 scope link
valid_lft forever preferred_lft forever
3: docker0: <BROADCAST,MULTICAST,UP,LOWER_UP> mtu 1500 qdisc noqueue state UP group default
link/ether 02:42:ca:cf:36:ae brd ff:ff:ff:ff:ff:ff
inet 172.17.0.1/16 scope global docker0
valid_lft forever preferred_lft forever
inet6 fe80::42:caff:fecf:36ae/64 scope link
valid_lft forever preferred_lft forever
7: vethbd1da82@if6: <BROADCAST,MULTICAST,UP,LOWER_UP> mtu 1500 qdisc noqueue master docker0 state UP group default
link/ether 36:6d:d6:bd:d5:d8 brd ff:ff:ff:ff:ff:ff link-netnsid 1
inet6 fe80::346d:d6ff:febd:d5d8/64 scope link
valid_lft forever preferred_lft forever
27: vethc65a98f@if26: <BROADCAST,MULTICAST,UP,LOWER_UP> mtu 1500 qdisc noqueue master docker0 state UP group default
link/ether e6:cf:79:d4:aa:7a brd ff:ff:ff:ff:ff:ff link-netnsid 0
inet6 fe80::e4cf:79ff:fed4:aa7a/64 scope link
valid_lft forever preferred_lft forever
57: veth714e7ab@if56: <BROADCAST,MULTICAST,UP,LOWER_UP> mtu 1500 qdisc noqueue master docker0 state UP group default
link/ether 1e:c2:a5:02:f6:ee brd ff:ff:ff:ff:ff:ff link-netnsid 3
inet6 fe80::1cc2:a5ff:fe02:f6ee/64 scope link
valid_lft forever preferred_lft forever