The Industrial Internet of Things (IIoT), also known as Industry 4.0, has brought a revolution in the production and manufacturing sectors as it assists in the automation of production management and reduces the manual effort needed in auditing and managing the pieces of machinery. IoT-enabled industries, in general, use sensors, smart meters, and actuators. Most of the time, the data held by these devices is surpassingly sensitive and private. This information might be modified, 1 stolen, or even the devices may be subjected to a Denial of Service (DoS) attack. As a consequence, the product quality may deteriorate or sensitive information may be leaked. An Intrusion Detection System (IDS), implemented in the network layer of IIoT, can detect attacks, thereby protecting the data and devices. Despite substantial advancements in attack detection in IIoT, existing works fail to detect certain attacks obfuscated from detectors resulting in a low detection performance. To address the aforementioned issue, we propose a Deep Learning-based Two Level Network Intrusion Detection System (DLTL-NIDS) for IIoT environment, emphasizing challenging attacks. The attacks that attain low accuracy or low precision in level-1 detection are marked as challenging attacks. Experimental results show that the proposed model, when tested against TON IoT, figures out the challenging attacks well and achieves an accuracy of 99.97%, precision of 95.62%, recall of 99.5%, and F1-score of 99.65%. The proposed DL-TLNIDS, when compared with state-of-art models, achieves a decrease in false alarm rate to 2.34% (flagging normal traffic as an attack) in IIoT.